4V7R

Yeast 80S ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the eukaryotic ribosome.

Ben-Shem, A.Jenner, L.Yusupova, G.Yusupov, M.

(2010) Science 330: 1203-1209

  • DOI: 10.1126/science.1194294
  • Primary Citation of Related Structures:  
    4V7R

  • PubMed Abstract: 
  • Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the ...

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.


    Organizational Affiliation

    IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France. adam@igbmc.fr



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Entity ID: 2
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40S ribosomal protein S0-A AACA252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 ABCB254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 ACCC240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5 ADCD225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-A AECE197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11 AFCF156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 AGCG151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-A AHCH137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 AICI142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16 AJCJ143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-A AKCK136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18 ALCL146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-A AMCM144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20 ANCN121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-A AOCO130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23 APCP145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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40S ribosomal protein S25-A AQCQ108Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-A ARCR67Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-A ASCS56Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein; RACK-1 ATCT319Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure AaBoCa20Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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Unassigned secondary structure AbCb105Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure AcCc93Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure AdCd35Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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Unassigned secondary structure AeBjDj21Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Af11Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure AhCh41Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L1 BADA217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L2 BBDB254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 BCDC387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-A BDDD362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 BEDE297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-A BFDF176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-A BGDG244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-A BHDH256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A BIDI191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 BJDJ221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-A BKDK174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-A BNDN138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A BODO204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A BPDP199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A BQDQ184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18 BRDR186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19 BSDS189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A BTDT160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23 BUDU137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A BVDV155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 BWDW142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A BXDX127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 BYDY149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30 BZDZ105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-A BaDa113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32 BbDb130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35 BcDc120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-A BdDd88Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39 BeDe51Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42 BfDf106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43 BgDg92Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure BhDh44Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure BiDi12Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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Unassigned secondary structure BkDk16Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Bl19Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Bm9Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Bn27Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Bp8Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Bq17Saccharomyces cerevisiaeMutation(s): 0 
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Unassigned secondary structure Br23Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L12 DL165Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein P0 DM312Saccharomyces cerevisiaeMutation(s): 0 
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18S ribosomal RNAA1, C11800Saccharomyces cerevisiae
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Entity ID: 29
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25S ribosomal RNAB1, D13396Saccharomyces cerevisiae S288C
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Entity ID: 30
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB2, D2121Saccharomyces cerevisiae
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(by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAB3, D3158Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OHX
Query on OHX

Download Ideal Coordinates CCD File 
A1, AL, AS, AT, Ac, B1, B2, B3, BC, BO, BT, Bd, Bg, C1, CI, CS, CT, D1, D2, D3, DC, DE, DJ, DO, DT, Dd, Dg
osmium (III) hexammine
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.280 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 437.11α = 90
b = 288.38β = 99.13
c = 306.56γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
DMmodel building
DMMultimodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
DMphasing
DMMultiphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-11-22
    Changes: Refinement description