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- PDB-5ndw: Crystal structure of aminoglycoside TC007 bound to the yeast 80S ... -

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Basic information

Entry
Database: PDB / ID: 5ndw
TitleCrystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome
Components
  • (40S ribosomal protein ...) x 31
  • (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 STM1
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / translation / 40S / 60S / 80S / eukaryote / RNA-protein complex / inhibitor / antibiotic / aminoglycoside
Function / homology
Function and homology information


triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / telomeric DNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / TOR signaling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / maturation of LSU-rRNA / 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) / ribosomal small subunit export from nucleus / translation regulator activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / telomere maintenance / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / mitochondrion / DNA binding
Similarity search - Function
Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site ...Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / S27a-like superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L34e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae, conserved site / Ribosomal protein L36e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / : / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L27e
Similarity search - Domain/homology
TC007 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 ...TC007 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Suppressor protein STM1 / Small ribosomal subunit protein uS11B / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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.
History
DepositionMar 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,188,1071565
Polymers6,141,731158
Non-polymers46,3761407
Water30,7161705
1
5: 25S ribosomal RNA
6: 18S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
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
e1: Ubiquitin-40S ribosomal protein S31
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
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
sM: Suppressor protein STM1
sR: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,092,532768
Polymers3,070,86579
Non-polymers21,667689
Water55831
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
1: 25S ribosomal RNA
2: 18S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
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
E1: Ubiquitin-40S ribosomal protein S31
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
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
SM: Suppressor protein STM1
SR: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,095,574797
Polymers3,070,86579
Non-polymers24,709718
Water66737
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)442.140, 298.760, 299.770
Angle α, β, γ (deg.)90.000, 99.490, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
RNA chain , 4 types, 8 molecules 15263748

#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 S288c (yeast) / References: REF: 831416132
#2: RNA chain 18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132
#3: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039024062
#4: 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 (brewer's yeast) / References: GenBank: 1102645687

+
40S ribosomal protein ... , 31 types, 62 molecules C0c0C1c1C2c2C3c3C4c4C5c5C6c6C7c7C8c8C9c9d0D0d1D1d2D2d3D3d4D4...

#5: Protein 40S ribosomal protein S10-A


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
#6: Protein 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17785.934 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
#7: Protein 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
#8: Protein 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
#9: Protein 40S ribosomal protein S14-B / 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
#10: Protein 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
#11: Protein 40S ribosomal protein S16-A / RP61R


Mass: 15659.216 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
#12: Protein 40S ribosomal protein S17-A / 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
#13: Protein 40S ribosomal protein S18-A


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
#14: Protein 40S ribosomal protein S19-A / 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
#15: Protein 40S ribosomal protein S20


Mass: 12190.175 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
#16: Protein 40S ribosomal protein S21-A / 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
#17: Protein 40S ribosomal protein S22-A / 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
#18: Protein 40S ribosomal protein S23-A / 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
#19: Protein 40S ribosomal protein S24-A / 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
#20: Protein 40S ribosomal protein S25-A / 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
#21: Protein 40S ribosomal protein S26-B


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
#22: Protein 40S ribosomal protein S27-A / 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
#23: Protein 40S ribosomal protein S28-A / 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
#24: Protein 40S ribosomal protein S29-A / 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
#25: Protein 40S ribosomal protein S30-A


Mass: 6878.217 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
#68: Protein 40S ribosomal protein S0-A / 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
#69: Protein 40S ribosomal protein S1-A / RP10A


Mass: 24498.365 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: P33442
#70: Protein 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
#71: Protein 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
#72: Protein 40S ribosomal protein S4-A / 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
#73: Protein 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
#74: Protein 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 27054.486 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: P0CX37
#75: Protein 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21000.492 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
#76: Protein 40S ribosomal protein S8-A / 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
#77: Protein 40S ribosomal protein S9-A / 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

-
Protein , 4 types, 8 molecules e1E1q0Q0sMSMsRSR

#26: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8388.049 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: P05759
#64: Protein 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
#78: Protein Suppressor protein STM1 / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / ...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
#79: Protein 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

+
60S ribosomal protein ... , 40 types, 80 molecules l2L2l3L3l4L4l5L5l6L6l7L7l8L8l9L9m0M0m1M1m3M3m4M4m5M5m6M6m7M7...

#27: Protein 60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27217.289 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
#28: Protein 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
#29: Protein 60S ribosomal protein L4-A / 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
#30: Protein 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
#31: Protein 60S ribosomal protein L6-A / 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
#32: Protein 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 25341.480 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
#33: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 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
#34: Protein 60S ribosomal protein L9-A / 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
#35: Protein 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
#36: Protein 60S ribosomal protein L11-B / 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
#37: Protein 60S ribosomal protein L13-A


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
#38: Protein 60S ribosomal protein L14-A


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
#39: Protein 60S ribosomal protein L15-A / 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
#40: Protein 60S ribosomal protein L16-A / 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
#41: Protein 60S ribosomal protein L17-A / 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
#42: Protein 60S ribosomal protein L18-A / 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
#43: Protein 60S ribosomal protein L19-A / 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
#44: Protein 60S ribosomal protein L20-A / 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
#45: Protein 60S ribosomal protein L21-A


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
#46: Protein 60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 11263.863 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
#47: Protein 60S ribosomal protein L23-A / 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
#48: Protein 60S ribosomal protein L24-A / 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
#49: Protein 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 13771.176 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
#50: Protein 60S ribosomal protein L26-A / L33 / YL33


Mass: 14134.588 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
#51: Protein 60S ribosomal protein L27-A


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
#52: Protein 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
#53: Protein 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
#54: Protein 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
#55: Protein 60S ribosomal protein L31-A / L34 / YL28


Mass: 12649.754 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
#56: Protein 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
#57: Protein 60S ribosomal protein L33-A / 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
#58: Protein 60S ribosomal protein L34-A


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
#59: Protein 60S ribosomal protein L35-A


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
#60: Protein 60S ribosomal protein L36-A / 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
#61: Protein 60S ribosomal protein L37-A / 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
#62: Protein 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
#63: 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
#65: Protein/peptide 60S ribosomal protein L41-A / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX86
#66: Protein 60S ribosomal protein L42-A / 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
#67: Protein 60S ribosomal protein L43-A / 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

-
Non-polymers , 4 types, 3112 molecules

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


Mass: 24.305 Da / Num. of mol.: 1365 / Source method: isolated from a natural source / Formula: Mg
#81: Chemical...
ChemComp-8UZ / TC007


Mass: 483.514 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C18H37N5O10
#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#83: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1705 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.32 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→147.832 Å / Num. obs: 814535 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 47.714 % / Biso Wilson estimate: 133.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.303 / Rrim(I) all: 0.306 / Χ2: 0.974 / Net I/σ(I): 13.97 / Num. measured all: 38865024 / Scaling rejects: 3776
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
3.7-3.86.9241.7650.9843058462468621850.3611.90499.5
3.8-3.913.6161.8371.4876486156192561750.5841.907100
3.9-424.0091.8542.08121977250817508040.7261.894100
4-4.122.5881.5532.47103862445985459810.7731.589100
4.1-4.230.6551.7532.95127667041651416470.8341.782100
4.2-4.337.5021.6333.54141858337828378270.891.656100
4.3-4.454.1751.5944.4187308934587345750.9191.609100
4.4-4.559.5931.4575.1187896331527315300.9391.47100
4.5-562.7481.0957.0576933031226321226070.9671.103100
5-5.564.7240.74110.74530998782049820410.9850.747100
5.5-661.2770.52514.21349444357037570270.9920.529100
6-7.565.2050.29322.6609284593450934410.9970.295100
7.5-1065.9070.13444.32374655856856568460.9990.135100
10-2562.7210.06775.342455592391653915110.068100
25-5064.5780.045116.211548592404239810.04699.8
50-7557.5810.063115.241318625422910.06390.2
75-10047.750.073105.42101624410.07571
100-14541.3330.08195.6899231240.9960.08277.4
145-15040.00529.84124310.00675
147.832-15013

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→147.832 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 16288 2 %
Rwork0.1919 798024 -
obs0.1927 814312 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 457.07 Å2 / Biso mean: 150.1253 Å2 / Biso min: 63.95 Å2
Refinement stepCycle: final / Resolution: 3.7→147.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms177720 218488 3803 103 400114
Biso mean--110.87 101.75 -
Num. residues----32778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009427946
X-RAY DIFFRACTIONf_angle_d1.382627207
X-RAY DIFFRACTIONf_chiral_restr0.06178573
X-RAY DIFFRACTIONf_plane_restr0.00741232
X-RAY DIFFRACTIONf_dihedral_angle_d20.55192859
LS refinement shell

Refine-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 (%)
3.7-3.7420.3445370.3348262702680799
3.742-3.78610.33785410.30522653927080100
3.7861-3.83220.32425410.29322648027021100
3.8322-3.88080.31955420.28562656227104100
3.8808-3.93180.29725410.26562651727058100
3.9318-3.98570.29695430.24872661327156100
3.9857-4.04260.2975410.2442649927040100
4.0426-4.1030.28195420.23852656027102100
4.103-4.16710.27625400.22682653927079100
4.1671-4.23540.26245440.21762657427118100
4.2354-4.30850.24575410.21342651327054100
4.3085-4.38680.25455430.20852659727140100
4.3868-4.47120.24845430.2032661127154100
4.4712-4.56250.2415410.19812654727088100
4.5625-4.66170.2365420.19122651527057100
4.6617-4.77010.24125430.19262663127174100
4.7701-4.88940.24395420.1872657327115100
4.8894-5.02160.21615420.17122658227124100
5.0216-5.16940.22885440.17232663927183100
5.1694-5.33630.20455440.16152660727151100
5.3363-5.5270.22355430.16632665727200100
5.527-5.74830.2195430.17192657427117100
5.7483-6.00990.22935420.1692661027152100
6.0099-6.32680.21755460.1582668527231100
6.3268-6.72320.20815420.15992663127173100
6.7232-7.24220.21145450.15592669827243100
7.2422-7.9710.2075460.15622673627282100
7.971-9.12430.19435450.15972670927254100
9.1243-11.4950.19255480.16052679527343100
11.495-147.95050.24255510.2133269612751299
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0960.03220.01540.03140.0150.00840.0882-0.0484-0.0083-0.0145-0.08380.0237-0.01130.00860.7746-0.0304-0.03290.7334-0.10690.8252-1.13150.996871.231
20.0819-0.0059-0.02090.0311-0.00790.00570.05230.0575-0.04070.0161-0.0706-0.0107-0.02670.00220.809-0.0060.00530.84790.00310.7022183.49467.3142225.9243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1segid *A0
2X-RAY DIFFRACTION2segid *B0

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