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, 6GQV, 6GQB

  • 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), ...

    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 P0P0189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L12-AP294Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AA252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3B386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AC361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5D296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AE175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AF222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AG233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AH191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10I220Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BJ169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AL193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AM136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AN203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AO197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AP183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AQ185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AR188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AS172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AT159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AU100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AV136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AW62Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25X121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AY126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AZ135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28a148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29b58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30c97Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-Ad109Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32e127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-Af106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-Ag112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-Ah119Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-Ai99Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-Aj87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38k77Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39l50Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40m52Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-Bn25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-Ao105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-Ap91Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-Aq206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-Ar214Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2s217Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3t223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-Au260Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5v206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-Aw223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-Ax184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-Ay199Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-Az185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AAA105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AAB153Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12AC124Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13AD150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-BAE127Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15AF124Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AAG141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-BAH125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AAI145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AAJ143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S20AK107Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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40S ribosomal protein S21-AAL87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S22-AAM129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S23-AAN144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S24-AAO134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S25-AAP70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S26-BAQ97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S27-AAR81Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
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40S ribosomal protein S28-AAS63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S29-AAT53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S30-AAU60Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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Guanine nucleotide-binding protein subunit beta-like proteinAV318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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Ubiquitin-40S ribosomal protein S31AW37Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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Elongation factor 2AX837Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 84
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60S ribosomal protein L1-ABA204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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25S ribosomal RNA13396Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNA3121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNA4158Saccharomyces cerevisiae
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Entity ID: 47
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18S ribosomal RNA21797Saccharomyces cerevisiae
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Entity ID: 82
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Transfer RNA - PheAY76Saccharomyces cerevisiae
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    • Entity ID: 83
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    Messenger RNAAZ7Saccharomyces cerevisiae
    Experimental Data & Validation

    Experimental Data

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

    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 

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