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- PDB-5ndv: Crystal structure of Paromomycin bound to the yeast 80S ribosome -

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Basic information

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


Ub-specific processing proteases / Translesion Synthesis by POLH / MAPK6/MAPK4 signaling / Negative regulation of MAPK pathway / Termination of translesion DNA synthesis / Translesion synthesis by POLI / Translesion synthesis by POLK / rt:r-sce-450408: / ABC-family proteins mediated transport / RMTs methylate histone arginines ...Ub-specific processing proteases / Translesion Synthesis by POLH / MAPK6/MAPK4 signaling / Negative regulation of MAPK pathway / Termination of translesion DNA synthesis / Translesion synthesis by POLI / Translesion synthesis by POLK / rt:r-sce-450408: / ABC-family proteins mediated transport / RMTs methylate histone arginines / rt:r-sce-187577: / SRP-dependent cotranslational protein targeting to membrane / rt:r-sce-174113: / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / GTP hydrolysis and joining of the 60S ribosomal subunit / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Dual Incision in GG-NER / rt:r-sce-8866652: / rt:r-sce-8866654: / Protein methylation / Neddylation / Peroxisomal protein import / Iron uptake and transport / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / rt:r-sce-5696394: / UCH proteinases / regulation of translational initiation in response to stress / triplex DNA binding / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / response to cycloheximide / invasive growth in response to glucose limitation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GDP-dissociation inhibitor activity / 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 / rRNA export from nucleus / 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) / regulation of translational fidelity / TOR signaling / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / oxidized purine DNA binding / oxidized purine nucleobase lesion DNA N-glycosylase activity / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / small-subunit processome / telomeric DNA binding / translational elongation / G-protein alpha-subunit binding / ribosomal small subunit biogenesis / ribosomal large subunit biogenesis / maturation of LSU-rRNA / protein kinase A catalytic subunit binding / polysome / cellular response to amino acid starvation / positive regulation of protein kinase activity / positive regulation of translational fidelity / assembly of large subunit precursor of preribosome / ribosome assembly / translational termination / positive regulation of DNA repair / maintenance of translational fidelity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / telomere maintenance / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / protein kinase C binding / cytoplasmic translation / modification-dependent protein catabolic process / macroautophagy / rRNA processing / large ribosomal subunit rRNA binding / protein tag
Ribosomal protein S10 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e ...Ribosomal protein S10 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / 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 S12/S23 / Ribosomal protein L30p/L7e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein S26e superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S4e, central domain superfamily / Ribosomal L39 protein / Ribosomal protein L34e / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal L40e family / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L29 protein / Ribosomal protein S10p/S20e / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / 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 L38e superfamily / Ribosomal protein S19e domain superfamily / Ribosomal protein S8e / Ribosomal protein S2, flavodoxin-like domain superfamily / 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 L31e domain superfamily / Ribosomal protein S19, superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 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 L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ribosomal protein L36e domain superfamily / Winged helix DNA-binding domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L10e/L16 superfamily
Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L14-A / 40S ribosomal protein S27-A / 60S ribosomal protein L16-A / 60S ribosomal protein L32 / 40S ribosomal protein S0-A / 40S ribosomal protein S7-A / 60S ribosomal protein L3 / 40S ribosomal protein S5 / 60S ribosomal protein L5 ...Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L14-A / 40S ribosomal protein S27-A / 60S ribosomal protein L16-A / 60S ribosomal protein L32 / 40S ribosomal protein S0-A / 40S ribosomal protein S7-A / 60S ribosomal protein L3 / 40S ribosomal protein S5 / 60S ribosomal protein L5 / 40S ribosomal protein S2 / 60S ribosomal protein L8-A / un:p14120: / 60S ribosomal protein L4-A / 60S ribosomal protein L41-B / Suppressor protein STM1 / 40S ribosomal protein S20 / 60S ribosomal protein L11-B / 40S ribosomal protein S14-B / 40S ribosomal protein S10-A / gb:1102645687: / gb:1039024062: / gb:834774822: / 40S ribosomal protein S28-A / 40S ribosomal protein S25-A / 60S ribosomal protein L19-A / 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 L37-A / 40S ribosomal protein S12 / 60S ribosomal protein L10 / 40S ribosomal protein S29-A / 60S ribosomal protein L35-A / 60S ribosomal protein L43-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 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 S1-A / 40S ribosomal protein S3 / 40S ribosomal protein S19-A / 40S ribosomal protein S16-A / 40S ribosomal protein S30-A / 60S ribosomal protein L18-A / 40S ribosomal protein S11-A / 60S ribosomal protein L2-A / 60S ribosomal protein L23-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S21-A / 40S ribosomal protein S23-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 / gb:874346701:
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsProkhorova, I. / Djumagulov, M. / Urzhumtsev, A. / Yusupov, M. / Yusupova, G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Authors: Prokhorova, I. / Altman, R.B. / Djumagulov, M. / Shrestha, J.P. / Urzhumtsev, A. / Ferguson, A. / Chang, C.T. / Yusupov, M. / Blanchard, S.C. / Yusupova, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 9, 2017 / Release: Dec 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 13, 2017Structure modelrepositoryInitial release
1.1Dec 20, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Dec 27, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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-B
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
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-B
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
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
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-B
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-B
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
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,227,4342398
Polymers6,120,840156
Non-polymers106,5952242
Water24,2481346
1
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
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-B
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-B
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
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,108,9751132
Polymers3,059,37578
Non-polymers49,5991054
Water46826
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
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-B
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
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-B
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
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Suppressor protein STM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,118,4591266
Polymers3,061,46478
Non-polymers56,9951188
Water57632
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)434.530, 293.330, 295.790
Angle α, β, γ (deg.)90.000, 97.400, 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 15374826

#1: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 834774822
#2: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1039024062
#3: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1102645687
#45: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 874346701

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

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


Mass: 26730.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#5: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#6: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#7: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26321
#8: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#9: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / RP11 / YL8


Mass: 25726.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05737
#10: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25656.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P17076
#11: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05738
#12: Protein/peptide 60S ribosomal protein L10 / / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41805
#13: Protein/peptide 60S ribosomal protein L11-B / Ribosome / L16 / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E757
#14: Protein/peptide 60S ribosomal protein L13-A / Ribosome


Mass: 21956.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#15: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36105
#16: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05748
#17: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26784
#18: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05740
#19: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#20: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#21: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#22: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#23: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / RP4 / YL31


Mass: 11135.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05749
#24: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#25: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04449
#26: Protein/peptide 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 13641.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#27: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / YL33


Mass: 14005.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05743
#28: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#29: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#30: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05747
#31: Protein/peptide 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 10902.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#32: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#33: Protein/peptide 60S ribosomal protein L32 /


Mass: 14478.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#34: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#35: Protein/peptide 60S ribosomal protein L34-A / Ribosome


Mass: 12608.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P87262
#36: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#37: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05745
#38: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#39: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#40: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#42: Protein/peptide 60S ribosomal protein L41-B / Ribosome / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX87
#43: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#44: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX25

-
Protein/peptide , 3 types, 6 molecules Q0q0SRsRSMsM

#41: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CH08
#77: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38011
#78: 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: 29916.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39015

+
40S ribosomal protein ... , 32 types, 62 molecules S0s0S1s1S2s2S3s3S4s4S5s5S6S7s7S8s8S9s9C0c0C1c1C2c2C3c3C4c4C5...

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


Mass: 22811.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32905
#47: Protein/peptide 40S ribosomal protein S1-A / Ribosome


Mass: 24498.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain RM11-1a) (yeast)
Strain: RM11-1a / References: UniProt: B3RHV0
#48: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 23212.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25443
#49: Protein/peptide 40S ribosomal protein S3 / / RP13 / YS3


Mass: 24702.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05750
#50: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#51: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / YS8


Mass: 22908.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#52: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#53: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40


Mass: 21158.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#54: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#55: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / YP28 / YS11


Mass: 21210.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#56: Protein/peptide 40S ribosomal protein S10-A / Ribosome


Mass: 12757.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08745
#57: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / YS12


Mass: 16588.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#58: Protein/peptide 40S ribosomal protein S12 /


Mass: 15488.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48589
#59: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#60: Protein/peptide 40S ribosomal protein S14-B / Ribosome / RP59B


Mass: 13560.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39516
#61: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01855
#62: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#63: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02407
#64: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#65: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07280
#66: Protein/peptide 40S ribosomal protein S20 /


Mass: 12447.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38701
#67: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0V8
#68: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#69: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#70: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#71: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / YS23


Mass: 8001.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E792
#72: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39939
#73: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#74: Protein/peptide 40S ribosomal protein S28-A / Ribosome / S33 / YS27


Mass: 7116.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9
#75: Protein/peptide 40S ribosomal protein S29-A / Ribosome / S36 / YS29


Mass: 6335.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41057
#76: Protein/peptide 40S ribosomal protein S30-A / Ribosome


Mass: 7006.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX33
#79: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / YS4


Mass: 24965.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37

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Non-polymers , 4 types, 3588 molecules

#80: Chemical...
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: C23H45N5O14 / Paromomycin
#81: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2139 / Source method: obtained synthetically / Formula: Mg / Magnesium
#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Zinc
#83: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1346 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→146.665 Å / Num. obs: 1098455 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.851 % / Biso Wilson estimate: 89.79 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.321 / Rrim(I) all: 0.332 / Χ2: 0.813 / Net I/σ(I): 7.37 / Num. measured all: 16313251 / Scaling rejects: 1169
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.46.6811.8760.9662712893958938620.3492.03199.9
3.4-3.510.5181.5861.4587749283447834280.5291.666100
3.5-3.614.3241.3122.13106587074433744130.7431.36100
3.6-3.715.2851.0872.71101732466562665550.8241.124100
3.7-3.816.1620.9013.4296752159879598630.880.93100
3.8-3.915.830.7334.0985136053783537800.9160.757100
3.9-416.6470.6234.8681017748670486680.9380.642100
4-4.516.3840.436.6930038631833631833410.9660.444100
4.5-516.2480.2849.5119073401174021173860.9810.294100
5-7.516.4310.20912.5336583412226672226460.9880.216100
7.5-1016.2720.15117.288564454431544280.9910.156100
10-2516.0270.13220.2460085437496374900.9920.136100
25-5016.1620.12522.8737238231423040.9910.12999.6
50-7511.3320.11619.1525612452260.9770.12392.2
75-1006.3330.15713.7926660420.9670.17170
100-12514.8570.12150.53208191410.12473.7
125-1507.1110.06138.97641490.9780.06764.3
146.665-15013

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→146.665 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 21962 2 %
Rwork0.203 1076077 -
Obs0.2039 1098039 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 426.97 Å2 / Biso mean: 102.7427 Å2 / Biso min: 22.11 Å2
Refinement stepCycle: final / Resolution: 3.3→146.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms174773 216058 7150 4 397985
Biso mean--67.33 43.47 -
Num. residues----32255
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.006424808
f_angle_d0.99622601
f_chiral_restr0.04978827
f_plane_restr0.00640591
f_dihedral_angle_d20.234192523
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.33750.38577290.3463356983642799
3.3375-3.37670.37227290.3363561036339100
3.3767-3.41790.33387310.31283582036551100
3.4179-3.46120.35167290.30353571236441100
3.4612-3.50670.32197300.27453581236542100
3.5067-3.55480.30247320.25773581236544100
3.5548-3.60560.30547300.25613580236532100
3.6056-3.65940.31397320.25283588736619100
3.6594-3.71660.2777310.23533581836549100
3.7166-3.77750.28097290.23493573036459100
3.7775-3.84270.28397310.23483583236563100
3.8427-3.91250.2857320.22823586836600100
3.9125-3.98780.25197300.20883578836518100
3.9878-4.06920.25947310.20563583836569100
4.0692-4.15770.24957320.19843583736569100
4.1577-4.25440.24237330.19673588336616100
4.2544-4.36080.23617300.18893578436514100
4.3608-4.47870.22747330.1823591436647100
4.4787-4.61050.22297290.18083578736516100
4.6105-4.75940.21547340.17663591736651100
4.7594-4.92950.22227310.17083586436595100
4.9295-5.12680.22597330.17323589436627100
5.1268-5.36020.21287340.16523591936653100
5.3602-5.64280.22057320.16593593936671100
5.6428-5.99630.21577330.16373590436637100
5.9963-6.45930.22887340.16973595036684100
6.4593-7.10930.21557350.1663600936744100
7.1093-8.1380.23257360.17023607136807100
8.138-10.25270.22637360.17923612936865100
10.2527-146.810.25657410.2271362493699099
Refinement TLS params.

S33: -0 Å ° / 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 °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.07360.0224-0.06190.0192-0.00670.04770.03020.07130.03580.0216-0.0091-0.00960.0213-0.0280.24980.00150.00520.2153-0.00530.18910.14251.875673.9283
20.1081-0.01660.00910.022-0.03080.0341-0.00180.0464-0.02650.0130.004-0.00920.00510.00920.2544-0.05-0.03130.2521-0.00920.274190.80165.3678223.0579
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION / Auth seq-ID: 0

IDRefine TLS-IDSelection details
11segid *A
22segid *B

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