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- PDB-4u4q: Crystal structure of Homoharringtonine bound to the yeast 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 4u4q
TitleCrystal structure of Homoharringtonine bound to the yeast 80S ribosome
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 40
  • (Unknown protein chain ...) x 3
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Suppressor protein STM1Silencer (firearms)
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / translation / 40S / 60S / 80S / eukaryote / RNA-protein complex / inhibitor / antibiotic
Function / homology
Function and homology information


Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of translational initiation in response to stress / triplex DNA binding / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / invasive growth in response to glucose limitation / rRNA export from nucleus / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / 90S preribosome / rescue of stalled ribosome / preribosome, large subunit precursor / oxidized purine DNA binding / translational elongation / response to cycloheximide / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / TOR signaling / regulation of translational fidelity / maturation of SSU-rRNA / oxidized purine nucleobase lesion DNA N-glycosylase activity / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / positive regulation of translational fidelity / ribosomal small subunit export from nucleus / maturation of LSU-rRNA / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / ribosomal large subunit biogenesis / small-subunit processome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / polysome / positive regulation of protein kinase activity / protein kinase A catalytic subunit binding / cellular response to amino acid starvation / ribosome assembly / translational termination / assembly of large subunit precursor of preribosome / cytoplasmic translation / positive regulation of DNA repair / maintenance of translational fidelity / small ribosomal subunit rRNA binding / telomere maintenance / ribosomal small subunit assembly / DNA-(apurinic or apyrimidinic site) endonuclease activity / mRNA 5'-UTR binding / protein kinase C binding / modification-dependent protein catabolic process / large ribosomal subunit rRNA binding / rRNA processing / protein tag / macroautophagy / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic stress granule / ribosome binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / damaged DNA binding / protein ubiquitination / translation / mRNA binding / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / DNA repair / nucleolus / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / mitochondrion / RNA binding / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
60s Acidic ribosomal protein / Ribosomal protein S4, KOW domain / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e ...60s Acidic ribosomal protein / Ribosomal protein S4, KOW domain / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal Protein L6, KOW domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L26/L24, KOW domain / Ribosomal protein L14, KOW motif / 60S ribosomal protein L10P, insertion domain / Ribosomal protein L23 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S14p/S29e / Ribosomal protein L5 / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L13 / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal L40e family / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / KOW motif / Ribosomal protein L3 / Ribosomal protein L10 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / WD domain, G-beta repeat / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L22e superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L36e / Ribosomal protein L31e domain superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ubiquitin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / 50S ribosomal protein L30e-like / 60S acidic ribosomal protein P0 / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S19e domain superfamily / Ribosomal protein L36e domain superfamily
60S ribosomal protein L16-A / Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L14-A / 40S ribosomal protein S27-A / 40S ribosomal protein S1-A / 40S ribosomal protein S0-A / 40S ribosomal protein S7-A / 40S ribosomal protein S2 / 40S ribosomal protein S5 / 60S ribosomal protein L5 ...60S ribosomal protein L16-A / Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L14-A / 40S ribosomal protein S27-A / 40S ribosomal protein S1-A / 40S ribosomal protein S0-A / 40S ribosomal protein S7-A / 40S ribosomal protein S2 / 40S ribosomal protein S5 / 60S ribosomal protein L5 / 60S ribosomal protein L8-A / 60S ribosomal protein L3 / 40S ribosomal protein S20 / 60S ribosomal protein L30 / 60S ribosomal protein L4-A / 60S ribosomal protein L41-A / 60S ribosomal protein L32 / 60S ribosomal protein L37-A / Suppressor protein STM1 / 40S ribosomal protein S10-A / gb:618731124: / gb:1262303: / 40S ribosomal protein S28-A / 40S ribosomal protein S25-A / 60S ribosomal protein L11-B / 60S ribosomal protein L13-A / 60S ribosomal protein L21-A / 40S ribosomal protein S26-B / 60S ribosomal protein L6-A / 40S ribosomal protein S15 / 60S ribosomal protein L34-A / 60S ribosomal protein L38 / 60S ribosomal protein L19-A / 40S ribosomal protein S12 / 60S ribosomal protein L10 / 40S ribosomal protein S29-A / 60S ribosomal protein L35-A / 40S ribosomal protein S8-A / 40S ribosomal protein S18-A / 60S ribosomal protein L9-A / 60S ribosomal protein L22-A / 60S ribosomal protein L15-A / 60S ribosomal protein L29 / 60S ribosomal protein L36-A / 60S ribosomal protein L33-A / 60S ribosomal protein L26-A / 60S ribosomal protein L17-A / 60S ribosomal protein L7-A / 40S ribosomal protein S13 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L39 / 60S ribosomal protein L25 / 60S ribosomal protein L24-A / 40S ribosomal protein S17-A / 60S ribosomal protein L28 / 40S ribosomal protein S9-A / 40S ribosomal protein S3 / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S16-A / 40S ribosomal protein S24-A / 60S ribosomal protein L18-A / 40S ribosomal protein S11-A / 60S ribosomal protein L2-A / 60S ribosomal protein L23-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S30-A / 40S ribosomal protein S23-A / 40S ribosomal protein S14-A / 60S ribosomal protein L42-A / 60S ribosomal protein L20-A / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L31-A / 60S ribosomal protein L27-A / 40S ribosomal protein S22-A / 40S ribosomal protein S21-A / 40S ribosomal protein S19-A / 60S ribosomal protein L43-A
tpg:329138943:
Biological speciesSaccharomyces cerevisiae ATCC 204508 / S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarreau de Loubresse, N. / Prokhorova, I. / Yusupova, G. / Yusupov, M.
CitationJournal: Nature / Year: 2014
Title: Structural basis for the inhibition of the eukaryotic ribosome.
Authors: Garreau de Loubresse, N. / Prokhorova, I. / Holtkamp, W. / Rodnina, M.V. / Yusupova, G. / Yusupov, M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4ul4, 4ul5, 4ul6, 4ul7, 4ul8
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 17, 2014Group: Other
Revision 1.3Jan 20, 2016Group: Derived calculations / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
S7: 40S ribosomal protein S7-A
S8: 40S ribosomal protein S8-A
S9: 40S ribosomal protein S9-A
C0: 40S ribosomal protein S10-A
C1: 40S ribosomal protein S11-A
C2: 40S ribosomal protein S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-A
C5: 40S ribosomal protein S15
C6: 40S ribosomal protein S16-A
C7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: 40S ribosomal protein S20
D1: 40S ribosomal protein S21-A
D2: 40S ribosomal protein S22-A
D3: 40S ribosomal protein S23-A
D4: 40S ribosomal protein S24-A
D5: 40S ribosomal protein S25-A
D6: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: Ubiquitin-40S ribosomal protein S31
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Suppressor protein STM1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
s9: 40S ribosomal protein S9-A
c0: 40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A
c2: 40S ribosomal protein S12
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-A
c5: 40S ribosomal protein S15
c6: 40S ribosomal protein S16-A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin-40S ribosomal protein S31
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m2: Unknown protein chain m2
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: 60S acidic ribosomal protein P0
p1: Unknown protein chain p1
p2: Unknown protein chain p2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,632,3172724
Polymers6,271,433162
Non-polymers360,8842562
Water0
1
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
S7: 40S ribosomal protein S7-A
S8: 40S ribosomal protein S8-A
S9: 40S ribosomal protein S9-A
C0: 40S ribosomal protein S10-A
C1: 40S ribosomal protein S11-A
C2: 40S ribosomal protein S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-A
C5: 40S ribosomal protein S15
C6: 40S ribosomal protein S16-A
C7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: 40S ribosomal protein S20
D1: 40S ribosomal protein S21-A
D2: 40S ribosomal protein S22-A
D3: 40S ribosomal protein S23-A
D4: 40S ribosomal protein S24-A
D5: 40S ribosomal protein S25-A
D6: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: Ubiquitin-40S ribosomal protein S31
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Suppressor protein STM1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,285,3401324
Polymers3,108,00179
Non-polymers177,3391245
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
s9: 40S ribosomal protein S9-A
c0: 40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A
c2: 40S ribosomal protein S12
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-A
c5: 40S ribosomal protein S15
c6: 40S ribosomal protein S16-A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin-40S ribosomal protein S31
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m2: Unknown protein chain m2
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: 60S acidic ribosomal protein P0
p1: Unknown protein chain p1
p2: Unknown protein chain p2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,346,9761400
Polymers3,163,43283
Non-polymers183,5441317
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)436.250, 286.920, 303.840
Angle α, β, γ (deg.)90.000, 98.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules 26153748

#1: RNA chain 18S ribosomal RNA / / RNA (1750-MER)


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: GenBank: 1262303
#36: RNA chain 25S ribosomal RNA / / RNA (3149-MER)


Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: TPG: 329138943
#37: RNA chain 5S ribosomal RNA / / RNA (121-MER)


Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: TPG: 329138943
#38: RNA chain 5.8S ribosomal RNA / / RNA (158-MER)


Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: GenBank: 618731124

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40S ribosomal protein ... , 32 types, 62 molecules S0s0S1s1S2s2S3s3S4s4S5s5S6s6S7s7S8s8S9s9C0c0C1c1C2c2C3c3C4c4...

#2: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A


Mass: 27920.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P32905
#3: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A


Mass: 28667.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P33442
#4: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 27359.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P25443
#5: Protein/peptide 40S ribosomal protein S3 / / RP13 / YS3


Mass: 26411.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05750
#6: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / YS6


Mass: 29338.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX35
#7: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / YS8


Mass: 24941.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P26783
#8: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX37
#9: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40


Mass: 21527.014 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P26786
#10: Protein/peptide 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX39
#11: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / YP28 / YS11


Mass: 22356.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: O13516
#12: Protein/peptide 40S ribosomal protein S10-A / Ribosome


Mass: 12771.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q08745
#13: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / YS12


Mass: 17668.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX47
#14: Protein/peptide 40S ribosomal protein S12 /


Mass: 15385.485 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P48589
#15: Protein/peptide 40S ribosomal protein S13 / / S27a / YS15


Mass: 16928.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05756
#16: Protein/peptide 40S ribosomal protein S14-A / Ribosome / RP59A


Mass: 14431.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P06367
#17: Protein/peptide 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / YS21


Mass: 15900.712 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q01855
#18: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R


Mass: 15746.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX51
#19: Protein/peptide 40S ribosomal protein S17-A / Ribosome / RP51A


Mass: 15820.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P02407
#20: Protein/peptide 40S ribosomal protein S18-A / Ribosome


Mass: 16940.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX55
#21: Protein/peptide 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P07280
#22: Protein/peptide 40S ribosomal protein S20 /


Mass: 13797.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P38701
#23: Protein/peptide 40S ribosomal protein S21-A / Ribosome / S26 / YS25


Mass: 9758.829 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0C0V8
#24: Protein/peptide 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0C0W1
#25: Protein/peptide 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / YS14


Mass: 15942.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX29
#26: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50


Mass: 15231.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX31
#27: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / YS23


Mass: 11936.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q3E792
#28: Protein/peptide 40S ribosomal protein S26-B / Ribosome


Mass: 11022.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P39939
#29: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / YS20


Mass: 8762.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P35997
#30: Protein/peptide 40S ribosomal protein S28-A / Ribosome / S33 / YS27


Mass: 7474.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q3E7X9
#31: Protein/peptide 40S ribosomal protein S29-A / Ribosome / S36 / YS29


Mass: 6544.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P41057
#32: Protein/peptide 40S ribosomal protein S30-A / Ribosome


Mass: 6779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX33
#80: Protein/peptide 40S ribosomal protein S30-A / Ribosome


Mass: 7006.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX33

+
Protein/peptide , 5 types, 9 molecules E1e1SRsRSMsMQ0q0p0

#33: Protein/peptide Ubiquitin-40S ribosomal protein S31


Mass: 8703.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05759
#34: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34710.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P38011
#35: Protein/peptide Suppressor protein STM1 / Silencer (firearms) / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1


Mass: 30048.010 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P39015
#76: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CH08
#82: Protein/peptide 60S acidic ribosomal protein P0 / A0 / L10E


Mass: 33617.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05317

+
60S ribosomal protein ... , 40 types, 80 molecules L2l2L3l3L4l4L5l5L6l6L7l7L8l8L9l9M0m0M1m1M3m3M4m4M5m5M6m6M7m7...

#39: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / RP8 / YL6


Mass: 27332.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX45
#40: Protein/peptide 60S ribosomal protein L3 / / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P14126
#41: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P10664
#42: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33633.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P26321
#43: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q02326
#44: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / RP11 / YL8


Mass: 27555.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05737
#45: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28044.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P17076
#46: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05738
#47: Protein/peptide 60S ribosomal protein L10 / / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25279.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P41805
#48: Protein/peptide 60S ribosomal protein L11-B / Ribosome / L16 / RP39 / YL22


Mass: 19654.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q3E757
#49: Protein/peptide 60S ribosomal protein L13-A / Ribosome


Mass: 22472.967 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q12690
#50: Protein/peptide 60S ribosomal protein L14-A / Ribosome


Mass: 15063.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P36105
#51: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05748
#52: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / RP22 / YL15


Mass: 22116.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P26784
#53: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / YL17


Mass: 20458.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05740
#54: Protein/peptide 60S ribosomal protein L18-A / Ribosome / RP28


Mass: 20478.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX49
#55: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX82
#56: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a


Mass: 20478.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX23
#57: Protein/peptide 60S ribosomal protein L21-A / Ribosome


Mass: 18148.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: Q02753
#58: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / RP4 / YL31


Mass: 13580.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05749
#59: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / YL32


Mass: 14362.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX41
#60: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P04449
#61: Protein/peptide 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 15656.417 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P04456
#62: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / YL33


Mass: 14134.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05743
#63: Protein/peptide 60S ribosomal protein L27-A / Ribosome


Mass: 15437.166 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0C2H6
#64: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P02406
#65: Protein/peptide 60S ribosomal protein L29 / / YL43


Mass: 6560.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05747
#66: Protein/peptide 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 11299.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P14120
#67: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / YL28


Mass: 12848.962 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0C2H8
#68: Protein/peptide 60S ribosomal protein L32 /


Mass: 14678.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P38061
#69: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05744
#70: Protein/peptide 60S ribosomal protein L34-A / Ribosome


Mass: 13542.001 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P87262
#71: Protein/peptide 60S ribosomal protein L35-A / Ribosome


Mass: 13811.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX84
#72: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / YL39


Mass: 11020.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P05745
#73: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P49166
#74: Protein/peptide 60S ribosomal protein L38 /


Mass: 8714.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P49167
#75: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


Mass: 6227.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P04650
#77: Protein/peptide 60S ribosomal protein L41-A / Ribosome / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX86
#78: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX27
#79: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / YL35


Mass: 9981.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
References: UniProt: P0CX25

+
Unknown protein chain ... , 3 types, 3 molecules m2p1p2

#81: Protein/peptide Unknown protein chain m2


Mass: 13634.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
#83: Protein/peptide Unknown protein chain p1


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)
#84: Protein/peptide Unknown protein chain p2


Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae ATCC 204508 / S288c (yeast)

+
Non-polymers , 4 types, 2562 molecules

#85: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1411 / Source method: obtained synthetically / Formula: Mg / Magnesium
#86: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 1133 / Source method: obtained synthetically / Formula: H12N6Os
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Zinc
#88: Chemical ChemComp-HMT / (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine / Homoharringtonine, Cephalotaxine, [3(R)]-4-methyl 2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate


Mass: 545.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H39NO9 / Omacetaxine mepesuccinate

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.69 Å / Num. obs: 1451516 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 9.37 % / Biso Wilson estimate: 74 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.341 / Rrim(I) all: 0.361 / Χ2: 0.962 / Net I/σ(I): 7.13 / Num. measured all: 13621629
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3-3.10.3393.5270.8812625311372471347983.72598.2
3.1-3.20.4982.2231.311135151207691187412.34798.3
3.2-3.30.6261.6521.7310018911064661047791.74298.4
3.3-3.40.7151.2862.1785342394284928761.36198.5
3.4-3.50.7921.0452.7179106783957827701.10298.6
3.5-3.60.850.8463.3170731274824738280.89398.7
3.6-3.80.9020.6454.2411612291270801255160.68298.8
3.8-40.9460.4655.789710941030381018880.4998.9
4-50.9790.2729.0828038253022572995030.28899.1
5-80.9920.1514.6522522082405042391380.15899.4
8-100.9960.09221.3934689238061379080.09799.6
10-200.9970.06926.3631586835210350510.07399.5
20-300.9980.05233.0932592361835810.05599
30-400.9970.05333.2470558868590.05797
400.9950.06211.8411276802800.07241.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: dev_1702)refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I

3u5b
PDB Unreleased entry

3u5c
PDB Unreleased entry

3u5d
PDB Unreleased entry

3u5e
PDB Unreleased entry

3u5f
PDB Unreleased entry

3u5g
PDB Unreleased entry

3u5h
PDB Unreleased entry

3u5i
PDB Unreleased entry


Resolution: 3→49.69 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 29019 2 %
Rwork0.2079 1422055 -
Obs0.2088 1451074 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 281.11 Å2 / Biso mean: 71.4458 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 3→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms179693 222116 11016 0 412825
Biso mean--111.67 --
Num. residues----32990
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.012438225
f_angle_d1.616650284
f_chiral_restr0.06479428
f_plane_restr0.00741812
f_dihedral_angle_d18.87194824
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.03410.37469590.3356469944795398
3.0341-3.06980.35619590.3173469564791598
3.0698-3.10720.34279590.2972470224798198
3.1072-3.14650.33089590.2868470004795998
3.1465-3.18790.2969610.2689471024806398
3.1879-3.23160.31919620.2657471484811098
3.2316-3.27780.31029600.2661470024796298
3.2778-3.32670.30619630.2525471904815398
3.3267-3.37860.29279620.2366471124807499
3.3786-3.4340.27679630.2268472124817599
3.434-3.49320.26759640.2187472504821499
3.4932-3.55670.25999640.2122471984816299
3.5567-3.62510.26279650.2083472714823699
3.6251-3.69910.25379660.1997473554832199
3.6991-3.77950.2369650.1921472854825099
3.7795-3.86740.23999680.1857474224839099
3.8674-3.96410.23289650.1821472804824599
3.9641-4.07120.23499670.1798474414840899
4.0712-4.19090.2289690.1762474734844299
4.1909-4.32610.23679690.1805474924846199
4.3261-4.48060.22499710.177475784854999
4.4806-4.65990.23099700.1757474884845899
4.6599-4.87180.22869720.1775476514862399
4.8718-5.12840.22239740.1802476964867099
5.1284-5.44940.22739740.1798476964867099
5.4494-5.86950.23529740.1887477684874299
5.8695-6.45910.25229770.2024478944887199
6.4591-7.39110.24619780.20684792748905100
7.3911-9.3020.25329820.21574806349045100
9.302-49.7020.27149780.2374480894906799
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6516-0.0799-0.55480.18420.04781.02170.0775-0.043-0.29980.1402-0.0388-0.00680.1522-0.020.04420.6796-0.43510.50931.1749-0.33311.181-110.5639-8.1706110.248
20.4925-0.45690.05340.7504-0.0520.25470.0096-0.273-0.34150.4316-0.1169-0.07360.4415-0.00710.09211.4677-0.18610.19080.98930.28880.9118-46.8274-27.8244139.102
30.53220.0681-0.13410.26250.10370.58750.02720.05280.09860.04670.01320.28360.0513-0.3388-0.06960.4746-0.10070.05461.1612-0.29061.1038-100.97159.631476.8885
40.36050.2444-0.01630.3151-0.03150.1998-0.0250.14660.06640.0533-0.01390.1801-0.0388-0.11320.01560.521-0.1567-0.00661.2083-0.34981.0114-99.533-29.161945.9702
50.3699-0.0652-0.17050.41240.0780.5829-0.03950.01320.14120.07980.03020.3814-0.1375-0.24960.01670.67280.33360.08050.9558-0.02121.0766-79.778981.156171.2332
60.3159-0.24520.15910.24720.09770.8566-0.0434-0.1748-0.16320.0555-0.02630.06030.2377-0.00240.02741.3187-0.39580.02410.7705-0.14620.9142-76.3364-77.139890.8232
70.282-0.0493-0.13910.4993-0.12920.3376-0.07160.08350.143-0.2205-0.1388-0.0453-0.13610.03390.22750.82660.24160.04910.74610.21590.9438-29.85698.065148.7616
80.6885-0.064-0.03620.4152-0.00060.6299-0.0253-0.24260.31090.2235-0.09770.0061-0.1405-0.1026-0.21650.7425-0.07290.53221.1342-0.47920.9322-97.491247.9664136.3787
90.40840.0154-0.00820.95470.22320.39580.1211-0.1180.20830.1618-0.07580.0269-0.1635-0.0216-0.09540.73470.13760.17510.5817-0.12350.7779-31.30689.004294.7774
100.4537-0.0557-0.00210.5250.13650.62990.09270.076-0.0373-0.17970.04120.293-0.1264-0.1452-0.10150.510.1716-0.171.3309-0.12031.2551-96.43841.564548.4198
110.27070.0297-0.00720.9463-0.20531.14650.07120.24720.0067-0.25170.08540.0277-0.0976-0.1118-0.13590.675-0.2471-0.03261.3634-0.14660.9417-86.5605-32.907214.0452
120.77890.50180.03251.06880.18750.3070.0715-0.2481-0.05660.2768-0.21760.00370.0037-0.05830.12110.65570.07860.17290.6997-0.11840.6247-52.113767.0661104.8748
131.0594-0.6733-0.15540.8767-0.34310.45790.05740.0350.1435-0.08670.04830.1022-0.0718-0.0841-0.0681.4222-0.0854-0.11.70640.08491.315-79.3825-25.6995-18.0958
140.4053-0.164-0.27770.45140.18820.59270.0142-0.19950.07280.3727-0.0710.1746-0.1553-0.24590.01910.7886-0.22470.23120.8965-0.14460.5489-60.442730.0918131.8568
150.0041-0.0317-0.00280.21340.03130.0021-0.0141-0.0966-0.2790.2479-0.07340.05820.11910.01410.03561.1635-0.28860.11110.46770.17111.1746-44.6563-39.5414116.0556
160.65710.1784-0.25121.15040.06541.0070.0184-0.0148-0.0836-0.1561-0.13020.01210.1691-0.03850.12990.5951-0.14640.09690.997-0.40541.0883-46.8675-69.963421.7614
170.42730.2821-0.29340.6201-0.34260.277-0.12010.0420.05170.2285-0.0076-0.06650.1985-0.09610.11411.0663-0.55550.24241.0223-0.44410.9996-97.8973-77.212573.4022
180.0954-0.04830.07940.36830.4990.85970.09150.2605-0.4277-0.12580.05250.00690.06050.0680.04210.5833-0.40990.28290.8849-0.35570.9918-111.9154-30.308298.4386
190.15080.1256-0.06860.4387-0.08210.0294-0.00630.0273-0.26790.18870.041-0.06720.22130.0389-0.00710.734-0.14740.05260.7857-0.33251.1945-49.2016-90.138849.1868
200.65870.25980.18350.81360.17780.4541-0.15260.1109-0.18830.0069-0.0453-0.18480.156-0.01070.05061.0122-0.5090.2660.8371-0.46521.3094-82.6746-95.134451.8331
212.09860.84270.6430.74830.27780.44780.00680.19040.038-0.2348-0.08530.4001-0.0483-0.13950.02390.6686-0.337-0.02911.2244-0.46971.2325-107.3842-55.738143.2622
220.7491-0.26350.30010.3333-0.0170.71740.08470.0340.14320.16330.03370.23690.0109-0.187-0.07440.648-0.12120.47351.312-0.38471.3441-110.857912.0749101.525
230.54740.00690.1460.3760.16340.6228-0.00480.15760.21350.1657-0.10340.23730.0728-0.21780.0280.49160.01240.29171.0328-0.18580.9402-89.925333.2252101.7716
240.2427-0.0181-0.08770.39620.24680.2138-0.06290.13920.0192-0.0770.01620.19770.00630.03090.0260.4016-0.01530.0610.6932-0.07360.5609-54.346121.373456.3351
250.6925-0.01580.32670.5592-0.02970.4369-0.11380.21720.0685-0.34020.07330.267-0.149-0.3074-0.00170.85290.392-0.18221.15390.09890.9963-73.958376.897633.6474
260.2841-0.32980.08930.376-0.10390.0260.0028-0.1727-0.0690.0991-0.0588-0.14050.04210.12560.0241.5272-0.251-0.06770.972-0.091.3821-63.597-102.092181.3144
270.4920.0219-0.01260.21240.18190.1749-0.0713-0.1737-0.29060.09190.03960.24690.3004-0.2501-0.00611.0312-0.33980.26960.91210.01011.1958-61.0348-22.8853109.6464
280.886-0.0705-0.00530.66090.0160.20490.0652-0.2334-0.01970.3199-0.0868-0.0512-0.0548-0.07570.01840.9306-0.23110.4311.0666-0.11810.9204-80.607117.3692141.2419
290.9028-0.20140.20511.0364-0.0121.3540.0294-0.3088-0.0610.3282-0.007-0.1932-0.12890.23970.01591.5799-0.42790.12531.1931-0.28870.8667-75.8859-57.028107.2673
301.2645-0.1327-0.4320.86590.14550.33540.10270.12730.1096-0.0229-0.04180.12130.0035-0.1396-0.03340.5666-0.31930.03551.0677-0.32410.9269-79.7481-47.543336.8035
310.8901-0.80820.10770.81620.00430.1578-0.1151-0.1829-0.2975-0.04580.07730.4628-0.0313-0.21030.02530.68660.03620.00391.1907-0.28160.8676-80.418812.79637.6126
320.15230.0747-0.13480.3630.43280.86340.1020.073-0.031-0.11820.1-0.03620.14530.0959-0.07531.144-0.02070.09031.6229-0.20390.9865-60.4661-42.7729-7.0694
330.6756-0.0303-0.13760.72610.19870.5491-0.057-0.09070.0420.2434-0.0070.17840.1521-0.10020.02770.9454-0.58710.35191.3519-0.40391.2384-132.3553-57.756686.9137
340.1349-0.1519-0.04690.0629-0.0114-0.03950.1434-0.01050.1207-0.0099-0.098-0.1410.01470.0195-0.05910.496-0.1488-0.03730.832-0.13120.9362-54.6764-40.199440.9489
350.1237-0.0286-0.23230.269-0.0740.51710.0566-0.1216-0.08330.1609-0.05170.11680.0027-0.0513-0.01950.4545-0.15680.10750.5551-0.04860.4203-2.7364-3.8277124.3591
360.25720.01090.00960.4053-0.04150.36960.08780.14060.21360.056-0.0579-0.024-0.2426-0.0576-0.04560.45170.10890.13160.43050.19130.59332.246561.262538.792
370.25940.0564-0.11760.1875-0.02480.16860.0156-0.0682-0.08060.077-0.0762-0.15480.04280.12570.07430.2716-0.0098-0.04570.45780.05930.423892.6481-24.66473.398
380.43010.04480.08330.6836-0.08520.24410.04520.1996-0.2195-0.13750.0555-0.00370.3944-0.1026-0.1070.8003-0.169-0.05830.5407-0.30080.792524.3299-93.114730.2334
390.16940.1491-0.10470.4776-0.26190.67550.0578-0.0183-0.0723-0.0905-0.1195-0.2214-0.04930.13680.08180.33170.00940.08460.56440.11680.504105.871512.158712.4415
400.5656-0.0535-0.28530.7920.25050.8803-0.04950.14690.0302-0.05730.0034-0.15790.1531-0.07850.05460.29740.00570.04020.3749-0.05380.305275.7324-31.263916.8504
410.3717-0.317-0.16150.94730.17030.3025-0.0652-0.2605-0.16180.4151-0.00080.1612-0.035300.06270.7507-0.16710.07990.81130.13470.383528.7421-39.6915161.1681
421.0731-0.3352-0.32330.20760.12890.20220.13320.34080.3106-0.19780.03020.038-0.13-0.2148-0.16270.48540.1540.00820.96310.30560.545120.452233.1705-8.7559
430.6598-0.07210.14730.5257-0.22910.4508-0.0640.1974-0.0701-0.16160.02430.09520.0367-0.2165-0.00380.3869-0.1089-0.07180.82-0.08340.426311.382-26.9512.4871
440.6043-0.0611-0.00760.43250.01050.36960.10350.007-0.1067-0.09950.06510.30380.2195-0.3954-0.12530.6124-0.251-0.12791.0021-0.21560.9862-12.5977-78.706829.8464
450.20770.06540.0060.3598-0.0860.4706-0.0279-0.1719-0.09410.1271-0.0749-0.09740.08420.17650.1070.4753-0.0271-0.06950.52450.19090.448771.3424-54.9574111.585
460.51780.25390.21840.21810.1040.27110.07620.33410.2087-0.0501-0.0374-0.0441-0.0323-0.0117-0.02090.4575-0.01390.06630.73380.10220.421968.429814.3154-15.7109
470.1493-0.0072-0.07560.01410.05580.25410.0356-0.1284-0.11280.1181-0.0366-0.03620.10480.0091-0.02320.4952-0.1647-0.01510.56850.14140.344942.4114-32.0521127.6303
480.28290.0203-0.00230.15990.11980.20080.05770.21130.12040.0518-0.0455-0.0215-0.0661-0.077-0.03150.31850.07490.05030.49070.18820.364955.978530.145912.3279
490.16840.01340.22650.65190.24060.46230.20880.07770.1814-0.1058-0.0534-0.12340.06940.1233-0.14010.4465-0.07860.03880.32020.01920.421373.31940.466567.8137
500.30070.02680.00350.21940.04520.1603-0.0175-0.0571-0.1460.0779-0.0222-0.02170.09790.01140.06550.32660.01370.03990.39040.07660.535980.8878-49.794365.5277
510.3895-0.07960.21130.4293-0.07740.49590.0188-0.08840.19060.0691-0.0202-0.0842-0.23690.01470.0120.7421-0.1270.0510.5584-0.18250.612437.09661.8851111.8507
520.76060.0634-0.52660.1544-0.07410.60240.0603-0.05730.10250.0417-0.14090.1677-0.0570.00020.06450.54330.02860.19750.6065-0.19470.6203-14.980952.0938118.6803
530.6741-0.4376-0.00810.37290.10070.0866-0.1004-0.1356-0.02020.1781-0.03750.2764-0.0204-0.20.07290.73460.10080.30120.8044-0.31520.7264-48.010358.4299133.5471
540.39890.2629-0.27980.6463-0.05870.355-0.02660.37430.0329-0.09740.07190.21840.1053-0.114-0.02090.36340.0029-0.00740.7468-0.0220.307148.7162-14.1193-4.7901
550.10880.1721-0.22470.2766-0.32580.6563-0.07970.0397-0.1196-0.09030.0072-0.00090.2496-0.13050.07380.4318-0.0716-0.03720.4693-0.16770.450746.166-54.855329.4598
560.4787-0.05010.61521.76210.14571.785-0.0644-0.0350.2037-0.0694-0.0671-0.1065-0.4440.00310.11551.22530.04410.01520.5291-0.31830.835524.193289.7425118.8346
570.49520.06880.09920.6884-0.12620.07040.20710.20980.1752-0.1334-0.07580.0953-0.0239-0.0749-0.08520.40540.16450.06720.55440.06990.4866-7.70245.571148.3741
580.5813-0.33070.36290.2359-0.20410.2273-0.11390.11410.6261-0.06760.0050.077-0.3869-0.24020.1490.80820.1670.1370.57040.10091.015-4.985181.337557.1694
590.4344-0.1860.04250.17890.04770.2484-0.0063-0.1673-0.03580.2813-0.0158-0.00240.06290.04840.05660.6272-0.19740.02660.7166-0.17920.336452.605624.9124143.3683
600.55590.01050.0250.42-0.0040.490.0143-0.15660.0090.11920.0599-0.1869-0.04850.2142-0.08070.4555-0.1985-0.12060.74750.0120.5002101.075511.6518114.1139
610.3559-0.167-0.1380.2523-0.05270.6594-0.0741-0.24670.02920.18580.02240.0298-0.04340.004-0.04890.8537-0.04270.38620.9515-0.22260.3586-7.551527.5035173.828
620.11970.1889-0.10640.4166-0.12570.2899-0.0243-0.0298-0.15310.03-0.0111-0.05040.06930.05830.01360.3302-0.0262-0.03550.37090.06910.431866.5579-54.046483.8942
630.03370.13260.05881.2501-0.10410.36060.0648-0.0795-0.1764-0.1056-0.0498-0.22720.08540.0073-0.0230.4246-0.055-0.03290.4858-0.08880.589156.0675-56.167451.2808
640.4635-0.31230.18210.3636-0.2691.05920.0774-0.13870.00620.0422-0.0250.27310.0786-0.20410.00410.6926-0.0650.29771.0544-0.12840.657-32.30423.4808152.7064
651.02170.4997-0.12571.75830.05281.17890.0698-0.01990.20130.0579-0.0121-0.1523-0.25840.1601-0.08740.521-0.03580.11370.2956-0.0320.598744.169772.068381.0967
661.097-0.00910.28710.2057-0.07990.46940.02230.13240.0128-0.0444-0.0048-0.1052-0.08690.176-0.04920.2754-0.03420.020.37810.07330.369489.7725-0.127557.7652
670.7505-0.0699-0.21410.77330.02650.98160.02990.070.00760.05160.0043-0.2120.0418-0.0002-0.02610.2992-0.02080.07120.51480.10710.32481.505314.35222.2171
680.6171-0.0507-0.42250.0734-0.13020.6245-0.1016-0.1705-0.1360.0847-0.04270.03120.097-0.08590.11510.6317-0.12550.17090.7623-0.19250.41366.234627.493144.4316
690.2308-0.1145-0.03180.80920.15620.10940.0097-0.3182-0.01660.24070.0732-0.13630.0093-0.0241-0.08020.564-0.0903-0.1120.8445-0.04760.347273.5335-0.7091141.8329
700.5478-0.2981-0.22780.31380.36170.55040.0753-0.0881-0.28410.1632-0.0620.18010.2031-0.274-0.03140.6928-0.269-0.01740.60250.20250.540136.6263-63.5946127.5161
710.2753-0.16410.07760.773-0.26720.7105-0.0426-0.11860.14950.225-0.0155-0.06030.11210.10460.02690.4542-0.137-0.01730.499-0.01440.318353.45052.726117.8828
721.15460.1154-0.37691.87610.33271.7236-0.023-0.09980.15010.14030.00750.0803-0.1767-0.07820.02410.9064-0.14750.09960.7972-0.3690.410829.045261.7575155.3508
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1610.10660.04210.09860.0794-0.00850.1233-0.1733-0.0879-0.2005-0.12080.05030.99550.0635-0.50290.04891.46550.113-0.16051.9035-0.06461.5684-2.339-0.147-24.7637
1620.2411-0.1914-0.16180.2560.11130.105-0.1424-0.76140.41330.547-0.2382-0.1864-0.4097-0.09980.27831.2516-0.03240.04311.3117-0.14621.000728.47190.796155.9703
1630.69910.4962-0.47670.87540.07040.68750.09580.0736-0.0851-0.04080.04230.1570.1833-0.002-0.10630.7299-0.0290.13980.8882-0.24130.8136-29.7496-15.68261.7681
1640.03180.00620.05940.00310.0240.1740.0521-0.2476-0.57250.09390.13650.69040.7288-0.6542-0.10981.9596-0.1263-0.00862.1118-0.36931.9672-21.3443-27.5943163.6868
1650.7822-0.2787-0.63181.5597-0.53180.92530.1678-0.45640.31990.60780.0433-0.7175-0.2390.3821-0.12951.3498-0.1246-0.04671.4042-0.05850.907212.1485-2.5062182.4438
166-0.00160.0140.01920.51690.63590.7759-0.0487-0.48320.52940.38880.26480.0175-0.4132-0.0693-0.14641.09510.20420.23510.874-0.33951.0996-4.588488.9308101.0396
1670.33250.15260.15730.42630.04210.13810.02280.337-0.2167-0.2025-0.01130.04160.207-0.134-0.05130.6159-0.2026-0.02710.7471-0.32850.528523.7732-66.80516.7835
1680.21850.006-0.0470.1937-0.13760.42770.0791-0.25870.07520.2282-0.0427-0.0651-0.1020.12660.00860.5254-0.1623-0.04080.6289-0.06280.362863.61897.6288126.4996
1690.26920.0328-0.06990.4629-0.05020.24440.0380.10860.1474-0.1046-0.07080.2309-0.175-0.26730.02970.53680.23150.02430.7886-0.05260.6972-54.261463.423362.934
1701.25670.8833-0.91333.56631.67132.4756-0.21450.37620.404-0.4777-0.10360.5466-0.5114-0.3890.19961.14420.4587-0.16251.21190.20141.0647-49.4469102.117434.5279
1711.9454-0.37540.14083.64180.84140.22140.0663-0.32430.31560.2791-0.00230.2447-0.3308-0.3116-0.02061.6650.3393-0.00321.4919-0.20481.7265-42.6558127.8022104.438
1720.89740.3588-0.29630.1608-0.1690.23230.00340.13330.54830.03760.00350.1467-0.5586-0.11190.01931.7294-0.07220.25591.6306-0.291.8233-59.181113.4522118.4098
1730.08920.2265-0.00050.5706-0.00460.0032-0.1873-0.2658-0.40890.3153-0.11360.43460.4321-0.26740.17662.4002-0.0977-0.3212.4882-0.10272.4113-112.29514.736227.8425
1740.20820.0689-0.01810.3032-0.18980.12-0.00230.1907-0.1238-0.27150.05210.17350.0133-0.2588-0.09160.79140.2652-0.15521.47740.01660.9456-83.765748.699324.7016
1750.50870.0339-0.07980.63580.01360.36840.0712-0.1374-0.10080.3379-0.15310.25830.0675-0.25460.04560.5834-0.17270.18120.7518-0.14310.6281-60.553910.4581106.4267
1760.59790.3744-0.22420.85380.57660.90640.03230.31020.3596-0.38760.20320.5113-0.4959-0.7013-0.13611.33850.29680.19741.7881-0.25512.0341-109.074258.094997.0254
1770.0046-0.00520.00810.0084-0.01580.0207-0.22040.0113-0.0394-0.2433-0.04140.61650.04-0.51730.17512.14880.15320.17012.3068-0.16222.1902-99.704579.4473109.2604
1780.0604-0.0623-0.20910.3395-0.15371.07310.11980.12180.16460.0213-0.06930.1609-0.34780.107-0.00010.63620.19130.13851.1651-0.21311.1601-80.175756.534978.8723
1790.07510.3771-0.09951.7185-0.48360.12660.26630.02820.19160.0714-0.11780.1718-0.4011-0.089-0.0841.3936-0.06640.41551.3245-0.47431.4899-63.772378.7801127.2369
1800.14280.1575-0.05850.35480.1750.15160.02190.1858-0.09720.1757-0.11850.07760.1442-0.28480.06640.6051-0.27890.05211.0415-0.3590.9589-74.5677-47.826256.4399
1810.350.0841-0.03070.58290.02780.28170.07820.1131-0.0823-0.0153-0.1187-0.0573-0.0169-0.1710.05630.41170.06610.06810.6403-0.10010.5621-35.676824.638874.6969
1820.17960.01020.00980.1344-0.01680.14140.01690.132-0.0091-0.05070.02410.01570.0368-0.0265-0.04320.361-0.0069-0.05690.26250.01490.2683140.14912.8926220.781
1831.6702-0.1229-0.08860.00730.00520.0034-0.0148-0.1478-0.41990.1920.2199-1.07960.16841.0657-0.1251.19250.225-0.30871.3869-0.04341.5852183.5055-36.6461298.7175
1840.40740.19920.43720.65460.14840.52460.23470.1443-0.03550.0799-0.3446-0.4203-0.01250.21810.20151.215-0.18180.02140.73720.13140.7834155.102521.832329.8263
1850.32860.1271-0.11390.1998-0.05120.038-0.11730.87390.4187-0.66110.0782-0.0187-0.45390.32580.04751.3791-0.03690.09661.52860.10531.0937170.3901-7.7077145.8597
1860.8166-0.4051-0.68861.32720.02260.67730.132-0.201-0.0440.1421-0.0064-0.12410.2301-0.0842-0.06020.6996-0.11430.05720.63880.09230.7386205.9486-10.8461249.122
1870.0081-0.01140.00570.0126-0.00860.00470.0315-0.0384-0.7847-0.00740.0208-0.34470.81670.4624-0.02072.11520.1729-0.08991.9705-0.09571.9947221.0704-35.4878151.6012
1881.41790.3756-0.48420.82770.60780.93490.06130.64950.3628-0.68110.01290.4912-0.254-0.2871-0.06081.6636-0.0226-0.08051.5801-0.23740.9539192.4699-13.6783124.4904
189-0.00070.0011-0.0060.0013-0.00830.0186-0.05670.49840.5025-0.37280.11410.0042-0.49770.1684-0.061.0321-0.15020.12630.89670.5011.0857187.496388.2941196.0923
1900.3105-0.2150.2530.2165-0.20430.043-0.0525-0.1176-0.13450.4150.12950.1091-0.0005-0.1084-0.08330.67080.0659-0.0770.2370.08940.397143.3173-56.9373290.7672
1910.2343-0.0555-0.07140.1550.06990.29240.02820.33120.0084-0.20640.06290.03270.0227-0.0708-0.03370.6118-0.0639-0.08570.74140.01620.3338128.66350.8617165.6177
1920.3234-0.0920.01980.60330.01890.1858-0.0332-0.01680.19870.1296-0.0563-0.2729-0.14730.06410.09620.5292-0.0906-0.09650.37230.0780.6325227.386169.0628248.2965
1931.406-0.6388-0.89682.5541-1.34351.9255-0.0562-0.42890.47910.5209-0.1512-0.304-0.40580.40370.13181.172-0.1276-0.31890.5756-0.18760.967214.9264109.4274272.7396
1940.42810.46740.00112.1864-1.08370.70190.13450.31510.3467-0.27650.0771-0.3542-0.36540.3461-0.12091.837-0.1443-0.13531.23630.30851.7125222.297131.6425201.7167
1950.00380.004-0.00120.00310.00040.0002-0.0169-0.1590.4689-0.0628-0.0932-0.1381-0.46820.06820.05392.41810.08470.03042.52110.08782.4792242.2403118.0111191.5937
1960.2704-0.61010.28121.7059-0.42160.4122-0.2050.3117-0.2144-0.3809-0.3122-0.45450.4020.44910.31161.9670.1163-0.59781.8253-0.06241.7522278.597525.5536297.369
1970.1945-0.01790.05070.13170.1330.1683-0.0315-0.25170.24410.2376-0.0941-0.0184-0.04290.10070.08470.9793-0.1164-0.3970.8284-0.01630.8991248.42158.012292.4764
1980.38320.09750.11720.60280.14420.1570.03680.1946-0.0753-0.0976-0.085-0.27750.00870.12130.06040.4270.0270.11790.52850.09160.7144244.517714.9003210.0607
1990.5312-0.11540.75630.2335-0.28021.4242-0.0181-0.58240.09450.52940.2051-0.2617-0.29240.6008-0.04641.4872-0.3101-0.15481.95250.22911.8942291.511159.5886236.1789
2000.78570.5525-0.31741.1456-0.69880.42710.13370.28910.0717-0.31010.1867-0.12-0.220.1326-0.12521.9691-0.37140.01991.75160.17631.7392272.938289.5604187.0961
2010.3596-0.0902-0.46970.47090.28490.6680.14010.02270.1341-0.0267-0.0545-0.2535-0.2922-0.1197-0.03970.5717-0.1012-0.02020.5790.24211.0587256.214363.0395238.6912
2020.8896-0.6665-0.21830.52980.1260.46320.0152-0.01820.31680.18990.0923-0.0593-0.4153-0.0798-0.01221.2524-0.05110.13831.20360.47521.1167249.957383.5039187.6081
203-0.2214-0.02420.1310.7898-0.3070.347-0.0308-0.04040.03840.23030.1-0.04560.1001-0.0637-0.04130.59440.09540.13550.51980.21990.823249.6751-40.3844264.5931
2040.54320.0107-0.04510.33290.04120.38040.02860.00370.1003-0.022-0.0619-0.008-0.17660.00680.05270.4242-0.0775-0.03580.34920.06190.3935209.183148.102235.1332
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth seq-IDAuth asym-ID
11segid S0A0
22segid S1A0
33segid S2A0
44segid S3A0
55segid S4A0
66segid S5A0
77segid S6A0
88segid S7A0
99segid S8A0
1010segid S9A0
1111segid S10A1 - 960
1212segid S11A2 - 1561
1313segid S12A20 - 1432
1414segid S13A2 - 1513
1515segid S14A11 - 1374
1616segid S15A8 - 1315
1717segid S16A3 - 1436
1818segid S17A2 - 1267
1919segid S18A2 - 1468
2020segid S19A2 - 1449
2121segid S20A15 - 1210
2222segid S21A1 - 871
2323segid S22A2 - 1302
2424segid S23A2 - 1453
2525segid S24A2 - 1354
2626segid S25A36 - 1055
2727segid S26A2 - 5006
2828segid S27A2 - 1017
2929segid S28A5 - 678
3030segid S29A4 - 999
3131segid S30A2 - 610
3232segid S31A82 - 5011
3333segid SRKA2 - 319R
3434segid STMA9 - 176M
3535segid L2A0
3636segid L3A0
3737segid L4A0
3838segid L5A0
3939segid L6A0
4040segid L7A0
4141segid L8A0
4242segid L9A0
4343segid L10A2 - 2210
4444segid L11A6 - 1741
4545segid L13A2 - 1943
4646segid L14A3 - 1384
4747segid L15A2 - 2045
4848segid L16A3 - 1996
4949segid L17A2 - 1847
5050segid L18A2 - 1868
5151segid L19A and resid 2:732 - 739
5252segid L19A and resid 74:12674 - 1269
5353segid L19A and resid 127:183127 - 1839
5454segid L20A1 - 1720
5555segid L21A2 - 1601
5656segid L22A9 - 1082
5757segid L23A2 - 1373
5858segid L24A1 - 984
5959segid L25A22 - 1425
6060segid L26A2 - 1276
6161segid L27A2 - 1367
6262segid L28A2 - 1498
6363segid L29A2 - 599
6464segid L30A9 - 1050
6565segid L31A4 - 1121
6666segid L32A2 - 1282
6767segid L33A2 - 1073
6868segid L34A2 - 1134
6969segid L35A2 - 1205
7070segid L36A2 - 1006
7171segid L37A2 - 1007
7272segid L38A2 - 788
7373segid L39A2 - 519
7474segid L40A77 - 5000
7575segid L41A1 - 251
7676segid L42A2 - 5012
7777segid L43A2 - 5013
7878segid S0B0
7979segid S1B0
8080segid S2B0
8181segid S3B0
8282segid S4B0
8383segid S5B0
8484segid S6B0
8585segid S7B0
8686segid S8B0
8787segid S9B0
8888segid S10B1 - 980
8989segid S11B2 - 1471
9090segid S12B20 - 1432
9191segid S13B2 - 1513
9292segid S14B10 - 1374
9393segid S15B4 - 1385
9494segid S16B2 - 1436
9595segid S17B2 - 1227
9696segid S18B2 - 1468
9797segid S19B2 - 1449
9898segid S20B12 - 1210
9999segid S21B1 - 871
100100segid S22B2 - 1302
101101segid S23B2 - 1453
102102segid S24B2 - 1354
103103segid S25B37 - 1055
104104segid S26B2 - 5006
105105segid S27B2 - 17
106106segid S28B5 - 678
107107segid S29B4 - 999
108108segid S30B2 - 630
109109segid S31B77 - 5011
110110segid SRKB2 - 319R
111111segid STMB23 - 174M
112112segid L2B0
113113segid L3B0
114114segid L4B0
115115segid L5B0
116116segid L6B0
117117segid L7B0
118118segid L8B0
119119segid L9B0
120120segid L10B2 - 2210
121121segid L11B6 - 1741
122122segid L12B9 - 1632
123123segid L13B2 - 1953
124124segid L14B2 - 1384
125125segid L15B2 - 2045
126126segid L16B3 - 1996
127127segid L17B2 - 1567
128128segid L18B2 - 1868
129129segid L19B and resid 2:732 - 739
130130segid L19B and resid 74:12674 - 1269
131131segid L19B and resid 127:183127 - 1839
132132segid L20B1 - 1720
133133segid L21B2 - 1601
134134segid L22B11 - 1082
135135segid L23B2 - 1373
136136segid L24B1 - 1354
137137segid L25B23 - 1425
138138segid L26B2 - 1276
139139segid L27B2 - 1367
140140segid L28B2 - 1498
141141segid L29B2 - 599
142142segid L30B6 - 1050
143143segid L31B4 - 1121
144144segid L32B2 - 1282
145145segid L33B2 - 1073
146146segid L34B2 - 1134
147147segid L35B2 - 1205
148148segid L36B2 - 1006
149149segid L37B2 - 5017
150150segid L38B2 - 788
151151segid L39B2 - 519
152152segid L40B77 - 5000
153153segid L41B1 - 251
154154segid L42B2 - 5012
155155segid L43B2 - 5013
156156segid LP0B3 - 2210
157157segid LP1B1 - 471
158158segid LP2B1 - 462
159159(segid 25SA and (not resid 1011:1039) and (not resid 1219:1288) and (not resid 1552:1583) and (not resid 2250:2266) and (not resid 2455:2502) and (not resid 2532:2547) and (not resid 2563:2578) and (not resid 3341:3364))0
160160(segid 25SA and resid 1011:1039)1011 - 10391
161161(segid 25SA and resid 1219:1288)1219 - 12881
162162(segid 25SA and resid 1552:1583)1552 - 15831
163163(segid 25SA and resid 2250:2266)2250 - 22661
164164(segid 25SA and resid 2532:2547)2532 - 25471
165165(segid 25SA and resid 2563:2578)2563 - 25781
166166(segid 25SA and resid 3341:3364)3341 - 33641
167167segid 5SA0
168168segid 58SA1 - 1584
169169((segid 18SA and resid 1:602) and (not resid 64:86) and (not resid 185:200) and (not resid 219:237) and (not resid 480:509) and (not resid 510:545))0
170170(segid 18SA and resid 64:86)64 - 862
171171(segid 18SA and resid 185:200)185 - 2002
172172(segid 18SA and resid 219:237)219 - 2372
173173(segid 18SA and resid 480:509)480 - 5092
174174(segid 18SA and resid 510:545)510 - 5452
175175((segid 18SA and resid 603:1106) and (not resid 640:694) and (not resid 698:742) and (not resid 743:765) and (not resid 810:855))0
176176(segid 18SA and resid 640:694)640 - 6942
177177(segid 18SA and resid 698:742)698 - 7422
178178(segid 18SA and resid 743:765)743 - 7652
179179(segid 18SA and resid 810:855)810 - 8552
180180(segid 18SA and resid 1107:1635)1107 - 16352
181181(segid 18SA and resid 1636:1799)1636 - 17992
182182(segid 25SB and (not resid 1011:1039) and (not resid 1219:1288) and (not resid 1552:1583) and (not resid 2250:2266) and (not resid 2455:2502) and (not resid 2532:2547) and (not resid 2563:2578) and (not resid 3341:3364))0
183183(segid 25SB and resid 1011:1039)1011 - 10395
184184(segid 25SB and resid 1219:1288)1219 - 12885
185185(segid 25SB and resid 1552:1583)1552 - 15835
186186(segid 25SB and resid 2250:2266)2250 - 22665
187187(segid 25SB and resid 2532:2547)2532 - 25475
188188(segid 25SB and resid 2563:2578)2563 - 25785
189189(segid 25SB and resid 3341:3364)3341 - 33645
190190segid 5SB0
191191segid 58SB1 - 1588
192192((segid 18SB and resid 1:602) and (not resid 64:86) and (not resid 185:200) and (not resid 219:237) and (not resid 480:509) and (not resid 510:545))0
193193(segid 18SB and resid 64:86)64 - 866
194194(segid 18SB and resid 185:200)185 - 2006
195195(segid 18SB and resid 219:237)219 - 2376
196196(segid 18SB and resid 480:509)480 - 5096
197197(segid 18SB and resid 510:545)510 - 5456
198198((segid 18SB and resid 603:1106) and (not resid 640:694) and (not resid 698:742) and (not resid 743:765) and (not resid 810:855))0
199199(segid 18SB and resid 640:694)640 - 6946
200200(segid 18SB and resid 698:742)698 - 7426
201201(segid 18SB and resid 743:765)743 - 7656
202202(segid 18SB and resid 810:855)810 - 8556
203203(segid 18SB and resid 1107:1635)1107 - 16356
204204(segid 18SB and resid 1636:1799)1636 - 17996

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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