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- PDB-4v7r: Yeast 80S ribosome. -

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Basic information

Entry
Database: PDB / ID: 4v7r
TitleYeast 80S ribosome.
Components
  • (40S ribosomal protein ...) x 19
  • (60S ribosomal protein ...) x 32
  • (Unassigned secondary ...) x 16
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
KeywordsRIBOSOME / Ribosomal rRNA and proteins / Translating the genetic code to proteins / eukaryotic / yeast
Function / homology
Function and homology information


negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / pre-mRNA 5'-splice site binding ...negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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 / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / 50S ribosomal protein L10, insertion domain superfamily / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein S19e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S17e, conserved site ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / 50S ribosomal protein L10, insertion domain superfamily / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein S19e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S17e, conserved site / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / : / Ribosomal protein L24e, conserved site / Ribosomal protein L1, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein S19e / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Ribosomal protein L30e, conserved site / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Ribosomal protein L44 / Ribosomal protein L23, N-terminal domain / Ribosomal Protein L6, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L31e, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal protein L44e signature. / Ribosomal protein L7A/L8 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L6, conserved site-2 / Ribosomal protein L14, KOW motif / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L14 / Ribosomal L37ae protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L39e, conserved site / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L6e signature. / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e
Similarity search - Domain/homology
osmium (III) hexammine / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...osmium (III) hexammine / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL15A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L18-A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2B / Small ribosomal subunit protein uS17B / Large ribosomal subunit protein eL18B / Small ribosomal subunit protein uS9B / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / 40S ribosomal protein S18-A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / 60S ribosomal protein L43-A / 60S ribosomal protein L1-B / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, SAD / Resolution: 4 Å
AuthorsBen-Shem, A. / Jenner, L. / Yusupova, G. / Yusupov, M.
CitationJournal: Science / Year: 2010
Title: Crystal structure of the eukaryotic ribosome.
Authors: Ben-Shem, A. / Jenner, L. / Yusupova, G. / Yusupov, M.
History
DepositionJul 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3O2Z, 3O30, 3O58, 3O5H
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: 18S ribosomal RNA
AA: 40S ribosomal protein S0-A
AB: 40S ribosomal protein S2
AC: 40S ribosomal protein S3
AD: 40S ribosomal protein S5
AE: 40S ribosomal protein S9-A
AF: 40S ribosomal protein S11
AG: 40S ribosomal protein S13
AH: 40S ribosomal protein S14-A
AI: 40S ribosomal protein S15
AJ: 40S ribosomal protein S16
AK: 40S ribosomal protein S17-A
AL: 40S ribosomal protein S18
AM: 40S ribosomal protein S19-A
AN: 40S ribosomal protein S20
AO: 40S ribosomal protein S22-A
AP: 40S ribosomal protein S23
AQ: 40S ribosomal protein S25-A
AR: 40S ribosomal protein S28-A
AS: 40S ribosomal protein S29-A
AT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Aa: Unassigned secondary structure
Ab: Unassigned secondary structure
Ac: Unassigned secondary structure
Ad: Unassigned secondary structure
Ae: Unassigned secondary structure
Af: Unassigned secondary structure
Ah: Unassigned secondary structure
B1: 25S ribosomal RNA
B2: 5S ribosomal RNA
B3: 5.8S ribosomal RNA
BA: 60S ribosomal protein L1
BB: 60S ribosomal protein L2
BC: 60S ribosomal protein L3
BD: 60S ribosomal protein L4-A
BE: 60S ribosomal protein L5
BF: 60S ribosomal protein L6-A
BG: 60S ribosomal protein L7-A
BH: 60S ribosomal protein L8-A
BI: 60S ribosomal protein L9-A
BJ: 60S ribosomal protein L10
BK: 60S ribosomal protein L11-A
BN: 60S ribosomal protein L14-A
BO: 60S ribosomal protein L15-A
BP: 60S ribosomal protein L16-A
BQ: 60S ribosomal protein L17-A
BR: 60S ribosomal protein L18
BS: 60S ribosomal protein L19
BT: 60S ribosomal protein L21-A
BU: 60S ribosomal protein L23
BV: 60S ribosomal protein L24-A
BW: 60S ribosomal protein L25
BX: 60S ribosomal protein L26-A
BY: 60S ribosomal protein L28
BZ: 60S ribosomal protein L30
Ba: 60S ribosomal protein L31-A
Bb: 60S ribosomal protein L32
Bc: 60S ribosomal protein L35
Bd: 60S ribosomal protein L37-A
Be: 60S ribosomal protein L39
Bf: 60S ribosomal protein L42
Bg: 60S ribosomal protein L43
Bh: Unassigned secondary structure
Bi: Unassigned secondary structure
Bj: Unassigned secondary structure
Bk: Unassigned secondary structure
Bl: Unassigned secondary structure
Bm: Unassigned secondary structure
Bn: Unassigned secondary structure
Bo: Unassigned secondary structure
Bp: Unassigned secondary structure
Bq: Unassigned secondary structure
Br: Unassigned secondary structure
C1: 18S ribosomal RNA
CA: 40S ribosomal protein S0-A
CB: 40S ribosomal protein S2
CC: 40S ribosomal protein S3
CD: 40S ribosomal protein S5
CE: 40S ribosomal protein S9-A
CF: 40S ribosomal protein S11
CG: 40S ribosomal protein S13
CH: 40S ribosomal protein S14-A
CI: 40S ribosomal protein S15
CJ: 40S ribosomal protein S16
CK: 40S ribosomal protein S17-A
CL: 40S ribosomal protein S18
CM: 40S ribosomal protein S19-A
CN: 40S ribosomal protein S20
CO: 40S ribosomal protein S22-A
CP: 40S ribosomal protein S23
CQ: 40S ribosomal protein S25-A
CR: 40S ribosomal protein S28-A
CS: 40S ribosomal protein S29-A
CT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Ca: Unassigned secondary structure
Cb: Unassigned secondary structure
Cc: Unassigned secondary structure
Cd: Unassigned secondary structure
Ch: Unassigned secondary structure
D1: 25S ribosomal RNA
D2: 5S ribosomal RNA
D3: 5.8S ribosomal RNA
DA: 60S ribosomal protein L1
DB: 60S ribosomal protein L2
DC: 60S ribosomal protein L3
DD: 60S ribosomal protein L4-A
DE: 60S ribosomal protein L5
DF: 60S ribosomal protein L6-A
DG: 60S ribosomal protein L7-A
DH: 60S ribosomal protein L8-A
DI: 60S ribosomal protein L9-A
DJ: 60S ribosomal protein L10
DK: 60S ribosomal protein L11-A
DL: 60S ribosomal protein L12
DM: 60S acidic ribosomal protein P0
DN: 60S ribosomal protein L14-A
DO: 60S ribosomal protein L15-A
DP: 60S ribosomal protein L16-A
DQ: 60S ribosomal protein L17-A
DR: 60S ribosomal protein L18
DS: 60S ribosomal protein L19
DT: 60S ribosomal protein L21-A
DU: 60S ribosomal protein L23
DV: 60S ribosomal protein L24-A
DW: 60S ribosomal protein L25
DX: 60S ribosomal protein L26-A
DY: 60S ribosomal protein L28
DZ: 60S ribosomal protein L30
Da: 60S ribosomal protein L31-A
Db: 60S ribosomal protein L32
Dc: 60S ribosomal protein L35
Dd: 60S ribosomal protein L37-A
De: 60S ribosomal protein L39
Df: 60S ribosomal protein L42
Dg: 60S ribosomal protein L43
Dh: Unassigned secondary structure
Di: Unassigned secondary structure
Dj: Unassigned secondary structure
Dk: Unassigned secondary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,851,649854
Polymers5,646,898139
Non-polymers204,751715
Water0
1
A1: 18S ribosomal RNA
AA: 40S ribosomal protein S0-A
AB: 40S ribosomal protein S2
AC: 40S ribosomal protein S3
AD: 40S ribosomal protein S5
AE: 40S ribosomal protein S9-A
AF: 40S ribosomal protein S11
AG: 40S ribosomal protein S13
AH: 40S ribosomal protein S14-A
AI: 40S ribosomal protein S15
AJ: 40S ribosomal protein S16
AK: 40S ribosomal protein S17-A
AL: 40S ribosomal protein S18
AM: 40S ribosomal protein S19-A
AN: 40S ribosomal protein S20
AO: 40S ribosomal protein S22-A
AP: 40S ribosomal protein S23
AQ: 40S ribosomal protein S25-A
AR: 40S ribosomal protein S28-A
AS: 40S ribosomal protein S29-A
AT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Aa: Unassigned secondary structure
Ab: Unassigned secondary structure
Ac: Unassigned secondary structure
Ad: Unassigned secondary structure
Ae: Unassigned secondary structure
Af: Unassigned secondary structure
Ah: Unassigned secondary structure
B1: 25S ribosomal RNA
B2: 5S ribosomal RNA
B3: 5.8S ribosomal RNA
BA: 60S ribosomal protein L1
BB: 60S ribosomal protein L2
BC: 60S ribosomal protein L3
BD: 60S ribosomal protein L4-A
BE: 60S ribosomal protein L5
BF: 60S ribosomal protein L6-A
BG: 60S ribosomal protein L7-A
BH: 60S ribosomal protein L8-A
BI: 60S ribosomal protein L9-A
BJ: 60S ribosomal protein L10
BK: 60S ribosomal protein L11-A
BN: 60S ribosomal protein L14-A
BO: 60S ribosomal protein L15-A
BP: 60S ribosomal protein L16-A
BQ: 60S ribosomal protein L17-A
BR: 60S ribosomal protein L18
BS: 60S ribosomal protein L19
BT: 60S ribosomal protein L21-A
BU: 60S ribosomal protein L23
BV: 60S ribosomal protein L24-A
BW: 60S ribosomal protein L25
BX: 60S ribosomal protein L26-A
BY: 60S ribosomal protein L28
BZ: 60S ribosomal protein L30
Ba: 60S ribosomal protein L31-A
Bb: 60S ribosomal protein L32
Bc: 60S ribosomal protein L35
Bd: 60S ribosomal protein L37-A
Be: 60S ribosomal protein L39
Bf: 60S ribosomal protein L42
Bg: 60S ribosomal protein L43
Bh: Unassigned secondary structure
Bi: Unassigned secondary structure
Bj: Unassigned secondary structure
Bk: Unassigned secondary structure
Bl: Unassigned secondary structure
Bm: Unassigned secondary structure
Bn: Unassigned secondary structure
Bo: Unassigned secondary structure
Bp: Unassigned secondary structure
Bq: Unassigned secondary structure
Br: Unassigned secondary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,905,961428
Polymers2,804,30273
Non-polymers101,660355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C1: 18S ribosomal RNA
CA: 40S ribosomal protein S0-A
CB: 40S ribosomal protein S2
CC: 40S ribosomal protein S3
CD: 40S ribosomal protein S5
CE: 40S ribosomal protein S9-A
CF: 40S ribosomal protein S11
CG: 40S ribosomal protein S13
CH: 40S ribosomal protein S14-A
CI: 40S ribosomal protein S15
CJ: 40S ribosomal protein S16
CK: 40S ribosomal protein S17-A
CL: 40S ribosomal protein S18
CM: 40S ribosomal protein S19-A
CN: 40S ribosomal protein S20
CO: 40S ribosomal protein S22-A
CP: 40S ribosomal protein S23
CQ: 40S ribosomal protein S25-A
CR: 40S ribosomal protein S28-A
CS: 40S ribosomal protein S29-A
CT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Ca: Unassigned secondary structure
Cb: Unassigned secondary structure
Cc: Unassigned secondary structure
Cd: Unassigned secondary structure
Ch: Unassigned secondary structure
D1: 25S ribosomal RNA
D2: 5S ribosomal RNA
D3: 5.8S ribosomal RNA
DA: 60S ribosomal protein L1
DB: 60S ribosomal protein L2
DC: 60S ribosomal protein L3
DD: 60S ribosomal protein L4-A
DE: 60S ribosomal protein L5
DF: 60S ribosomal protein L6-A
DG: 60S ribosomal protein L7-A
DH: 60S ribosomal protein L8-A
DI: 60S ribosomal protein L9-A
DJ: 60S ribosomal protein L10
DK: 60S ribosomal protein L11-A
DL: 60S ribosomal protein L12
DM: 60S acidic ribosomal protein P0
DN: 60S ribosomal protein L14-A
DO: 60S ribosomal protein L15-A
DP: 60S ribosomal protein L16-A
DQ: 60S ribosomal protein L17-A
DR: 60S ribosomal protein L18
DS: 60S ribosomal protein L19
DT: 60S ribosomal protein L21-A
DU: 60S ribosomal protein L23
DV: 60S ribosomal protein L24-A
DW: 60S ribosomal protein L25
DX: 60S ribosomal protein L26-A
DY: 60S ribosomal protein L28
DZ: 60S ribosomal protein L30
Da: 60S ribosomal protein L31-A
Db: 60S ribosomal protein L32
Dc: 60S ribosomal protein L35
Dd: 60S ribosomal protein L37-A
De: 60S ribosomal protein L39
Df: 60S ribosomal protein L42
Dg: 60S ribosomal protein L43
Dh: Unassigned secondary structure
Di: Unassigned secondary structure
Dj: Unassigned secondary structure
Dk: Unassigned secondary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,945,688426
Polymers2,842,59766
Non-polymers103,091360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)437.110, 288.380, 306.560
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules A1C1B1D1B2D2B3D3

#1: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: Z75578
#29: 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: GenBank: BK006945.1
#30: 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: J01360.1, GenBank: AE016820.4
#31: 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: HQ026735.1

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40S ribosomal protein ... , 19 types, 38 molecules AACAABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCO...

#2: Protein 40S ribosomal protein S0-A / Ribosome


Mass: 28051.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#3: Protein 40S ribosomal protein S2 /


Mass: 27490.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#4: Protein 40S ribosomal protein S3 /


Mass: 26542.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750
#5: Protein 40S ribosomal protein S5 /


Mass: 25072.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783
#6: Protein 40S ribosomal protein S9-A / Ribosome


Mass: 22487.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#7: Protein 40S ribosomal protein S11 /


Mass: 17785.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26781, UniProt: P0CX48*PLUS
#8: Protein 40S ribosomal protein S13 /


Mass: 17059.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#9: Protein 40S ribosomal protein S14-A / Ribosome


Mass: 14562.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367
#10: Protein 40S ribosomal protein S15 /


Mass: 16031.907 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855
#11: Protein 40S ribosomal protein S16 /


Mass: 15877.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40213, UniProt: P0CX52*PLUS
#12: Protein 40S ribosomal protein S17-A / Ribosome


Mass: 15820.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02407
#13: Protein 40S ribosomal protein S18 /


Mass: 17071.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35271, UniProt: P0CX56*PLUS
#14: Protein 40S ribosomal protein S19-A / Ribosome


Mass: 15942.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280
#15: Protein 40S ribosomal protein S20 /


Mass: 13929.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#16: Protein 40S ribosomal protein S22-A / Ribosome


Mass: 14650.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#17: Protein 40S ribosomal protein S23 /


Mass: 16073.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32827, UniProt: P0CX30*PLUS
#18: Protein 40S ribosomal protein S25-A / Ribosome


Mass: 12067.272 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792
#19: Protein 40S ribosomal protein S28-A / Ribosome


Mass: 7605.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9
#20: Protein 40S ribosomal protein S29-A / Ribosome


Mass: 6675.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057

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Protein , 2 types, 3 molecules ATCTDM

#21: Protein Guanine nucleotide-binding protein subunit beta-like protein; RACK-1 / Receptor of activated protein kinase C 1 / RACK1 / Receptor for activated C kinase


Mass: 34841.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011
#73: Protein 60S acidic ribosomal protein P0 / / A0 / L10E


Mass: 33798.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317

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Unassigned secondary ... , 16 types, 27 molecules AaBoCaAbCbAcCcAdCdAeBjDjAfAhChBhDhBiDiBkDkBlBmBnBpBqBr

#22: Protein/peptide Unassigned secondary structure


Mass: 1720.111 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#23: Protein Unassigned secondary structure


Mass: 8954.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein Unassigned secondary structure


Mass: 7932.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#25: Protein/peptide Unassigned secondary structure


Mass: 2996.685 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#26: Protein/peptide Unassigned secondary structure


Mass: 1805.216 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#27: Protein/peptide Unassigned secondary structure


Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#28: Protein/peptide Unassigned secondary structure


Mass: 3507.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#63: Protein/peptide Unassigned secondary structure


Mass: 3762.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#64: Protein/peptide Unassigned secondary structure


Mass: 1039.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#65: Protein/peptide Unassigned secondary structure


Mass: 1379.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#66: Protein/peptide Unassigned secondary structure


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#67: Protein/peptide Unassigned secondary structure


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#68: Protein/peptide Unassigned secondary structure


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#69: Protein/peptide Unassigned secondary structure


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#70: Protein/peptide Unassigned secondary structure


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#71: Protein/peptide Unassigned secondary structure


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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60S ribosomal protein ... , 32 types, 63 molecules BADABBDBBCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBNDNBODOBPDPBQDQ...

#32: Protein 60S ribosomal protein L1 / / L10a


Mass: 24524.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53030, UniProt: P0CX43*PLUS
#33: Protein 60S ribosomal protein L2 / / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05736, UniProt: P0CX46*PLUS
#34: Protein 60S ribosomal protein L3 /


Mass: 43850.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#35: Protein 60S ribosomal protein L4-A / Ribosome


Mass: 39159.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#36: Protein 60S ribosomal protein L5 /


Mass: 33792.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#37: Protein 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 (brewer's yeast) / References: UniProt: Q02326
#38: Protein 60S ribosomal protein L7-A / Ribosome / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#39: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 /


Mass: 28175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#40: Protein 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 (brewer's yeast) / References: UniProt: P05738
#41: Protein 60S ribosomal protein L10 /


Mass: 25410.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805
#42: Protein 60S ribosomal protein L11-A / Ribosome / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W9
#43: Protein 60S ribosomal protein L14-A / Ribosome


Mass: 15195.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#44: Protein 60S ribosomal protein L15-A / Ribosome / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#45: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#46: Protein 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 (brewer's yeast) / References: UniProt: P05740
#47: Protein 60S ribosomal protein L18 / / RP28


Mass: 20609.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07279, UniProt: P0CX50*PLUS
#48: Protein 60S ribosomal protein L19 / / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05735, UniProt: P0CX83*PLUS
#49: Protein 60S ribosomal protein L21-A / Ribosome


Mass: 18279.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#50: Protein 60S ribosomal protein L23 / / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04451, UniProt: P0CX42*PLUS
#51: Protein 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 (brewer's yeast) / References: UniProt: P04449
#52: Protein 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#53: Protein 60S ribosomal protein L26-A / Ribosome / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#54: Protein 60S ribosomal protein L28 / / L27a / L29 / RP44 / RP62 / YL24


Mass: 16762.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#55: Protein 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#56: Protein 60S ribosomal protein L31-A / Ribosome / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#57: Protein 60S ribosomal protein L32 /


Mass: 14809.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#58: Protein 60S ribosomal protein L35 /


Mass: 13942.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39741, UniProt: P0CX84*PLUS
#59: Protein 60S ribosomal protein L37-A / Ribosome / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#60: Protein 60S ribosomal protein L39 / / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#61: Protein 60S ribosomal protein L42 /


Mass: 12246.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02405, UniProt: P0CX28*PLUS
#62: Protein 60S ribosomal protein L43 / / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49631, UniProt: P0CX26*PLUS
#72: Protein 60S ribosomal protein L12 / / L15 / YL23


Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17079, UniProt: P0CX53*PLUS

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Non-polymers , 1 types, 715 molecules

#74: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 715 / Source method: obtained synthetically / Formula: H12N6Os

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7
Details: PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2009
RadiationMonochromator: 0.999 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 4→268 Å / Num. all: 630832 / Num. obs: 619044 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
4-4.151184.5
4.15-4.352197.9

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
DMmodel building
DMMultimodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
DMphasing
DMMultiphasing
RefinementMethod to determine structure: molecular replacement, SAD / Resolution: 4→268 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.341 12352 RANDOM 2%
Rwork0.278 --
obs0.28 605235 -
all-619044 -
Refinement stepCycle: LAST / Resolution: 4→268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14656 38107 2485 0 55248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfhenix bond distance0.011
X-RAY DIFFRACTIONfhenix bond angle degree1.4

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