6GQV

Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance.

Pellegrino, S., Demeshkina, N., Mancera-Martinez, E., Melnikov, S., Simonetti, A., Myasnikov, A., Yusupov, M., Yusupova, G., Hashem, Y.

(2018) J Mol Biol 430: 2677-2687

  • DOI: 10.1016/j.jmb.2018.06.006
  • Primary Citation of Related Structures:  
    6GQ1, 6GQB, 6GQV

  • PubMed Abstract: 

    • One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species ...

    One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.

    Organizational Affiliation: 

    ARNA, U1212 Université de Bordeaux, Institut Européen de Chimie et de Biologie (IECB) Inserm, Pessac 33600, France. Electronic address: yaser.hashem@u-bordeaux.fr.



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60S acidic ribosomal protein P0D [auth P0]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L12-AE [auth P2]94Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AF [auth A]252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3G [auth B]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AH [auth C]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5I [auth D]296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AJ [auth E]175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AK [auth F]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AL [auth G]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BO [auth J]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AT [auth P]183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AU [auth Q]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AV [auth R]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AW [auth S]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AX [auth T]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AY [auth U]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AZ [auth V]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AAA [auth W]62Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25BA [auth X]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-ACA [auth Y]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-ADA [auth Z]135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28EA [auth a]148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29FA [auth b]58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30GA [auth c]97Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-AHA [auth d]109Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32IA [auth e]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-AJA [auth f]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-AKA [auth g]112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-ALA [auth h]119Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-AMA [auth i]99Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-ANA [auth j]87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38OA [auth k]77Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39PA [auth l]50Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40QA [auth m]52Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-BRA [auth n]25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-ASA [auth o]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-ATA [auth p]91Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-AVA [auth q]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AWA [auth r]214Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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40S ribosomal protein S2XA [auth s]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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40S ribosomal protein S3YA [auth t]223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
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40S ribosomal protein S4-AZA [auth u]260Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
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40S ribosomal protein S5AB [auth v]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
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40S ribosomal protein S6-ABB [auth w]223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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40S ribosomal protein S7-ACB [auth x]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
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40S ribosomal protein S8-ADB [auth y]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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40S ribosomal protein S9-AEB [auth z]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
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40S ribosomal protein S10-AFB [auth AA]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
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40S ribosomal protein S11-AGB [auth AB]153Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12HB [auth AC]124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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40S ribosomal protein S13IB [auth AD]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S14-BJB [auth AE]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S15KB [auth AF]124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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40S ribosomal protein S16-ALB [auth AG]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S17-BMB [auth AH]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S18-ANB [auth AI]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S19-AOB [auth AJ]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20PB [auth AK]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S21-AQB [auth AL]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S22-ARB [auth AM]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S23-ASB [auth AN]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S24-ATB [auth AO]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S25-AUB [auth AP]70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S26-BVB [auth AQ]97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-AWB [auth AR]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S28-AXB [auth AS]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S29-AYB [auth AT]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S30-AZB [auth AU]60Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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Guanine nucleotide-binding protein subunit beta-like proteinAC [auth AV]318Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31BC [auth AW]37Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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Elongation factor 2CC [auth AX]837Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 84
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60S ribosomal protein L1-AFC [auth BA]204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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25S ribosomal RNAA [auth 1]3,396Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNAB [auth 3]121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNAC [auth 4]158Saccharomyces cerevisiae
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Entity ID: 47
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18S ribosomal RNAUA [auth 2]1,797Saccharomyces cerevisiae
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Entity ID: 82
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Transfer RNA - PheDC [auth AY]76Saccharomyces cerevisiae
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Entity ID: 83
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Messenger RNAEC [auth AZ]7Saccharomyces cerevisiae
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE		CC [auth AX]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
FranceANR-15-CE11-0021-01
FranceFRM-DBF20160635745
ERC-294312
FranceANR-14-ACHN-0024

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references