8CDR

Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

mRNA reading frame maintenance during eukaryotic ribosome translocation.

Milicevic, N.Jenner, L.Myasnikov, A.Yusupov, M.Yusupova, G.

(2024) Nature 625: 393-400

  • DOI: https://doi.org/10.1038/s41586-023-06780-4
  • Primary Citation of Related Structures:  
    8CCS, 8CDL, 8CDR, 8CEH, 8CF5, 8CG8, 8CGN, 8CIV, 8CKU, 8CMJ

  • PubMed Abstract: 

    One of the most critical steps of protein synthesis is coupled translocation of messenger RNA (mRNA) and transfer RNAs (tRNAs) required to advance the mRNA reading frame by one codon. In eukaryotes, translocation is accelerated and its fidelity is maintained by elongation factor 2 (eEF2) 1,2 . At present, only a few snapshots of eukaryotic ribosome translocation have been reported 3-5 . Here we report ten high-resolution cryogenic-electron microscopy (cryo-EM) structures of the elongating eukaryotic ribosome bound to the full translocation module consisting of mRNA, peptidyl-tRNA and deacylated tRNA, seven of which also contained ribosome-bound, naturally modified eEF2. This study recapitulates mRNA-tRNA 2 -growing peptide module progression through the ribosome, from the earliest states of eEF2 translocase accommodation until the very late stages of the process, and shows an intricate network of interactions preventing the slippage of the translational reading frame. We demonstrate how the accuracy of eukaryotic translocation relies on eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs. Our findings shed light on the mechanism of translation arrest by the anti-fungal eEF2-binding inhibitor, sordarin. We also propose that the sterically constrained environment imposed by diphthamide, a conserved eukaryotic posttranslational modification in eEF2, not only stabilizes correct Watson-Crick codon-anticodon interactions but may also uncover erroneous peptidyl-tRNA, and therefore contribute to higher accuracy of protein synthesis in eukaryotes.


  • Organizational Affiliation

    Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AA [auth 0]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AB [auth 1]108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26C [auth 2]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AD [auth 3]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AE [auth 4]67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
HLJ1_G0030400.mRNA.1.CDS.1F [auth 5]56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AG [auth 6]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinH [auth 7]319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31I [auth 8]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AJ [auth A]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2L [auth Aa]842Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AM [auth B]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AP [auth C]186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AS [auth D]189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0T [auth DD]312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AV [auth E]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AW [auth EE]254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12-AX [auth Ee]165Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AY [auth F]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3Z [auth FF]387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AAA [auth G]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-ABA [auth GG]362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-ACA [auth H]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5DA [auth HH]297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AEA [auth I]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AFA [auth II]176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25GA [auth J]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AHA [auth JJ]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AIA [auth K]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AJA [auth KK]256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AKA [auth L]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ALA [auth LL]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28MA [auth M]149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10NA [auth MM]221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29OA [auth N]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-APA [auth NN]174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30QA [auth O]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-ARA [auth OO]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ASA [auth P]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-ATA [auth PP]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
dipeptideUA [auth Pp]2Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32VA [auth Q]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AWA [auth QQ]204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AXA [auth R]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AYA [auth S]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AZA [auth T]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AAB [auth U]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ABB [auth V]88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38CB [auth W]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39DB [auth X]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40EB [auth Y]128Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AFB [auth Z]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AGB [auth a]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AHB [auth b]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AJB [auth d]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AKB [auth e]255Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2LB [auth f]254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
RPS3 isoform 1MB [auth g]240Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-ANB [auth h]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5OB [auth i]225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-APB [auth j]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AQB [auth k]190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-BRB [auth l]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-ASB [auth m]197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-ATB [auth n]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AUB [auth o]156Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13VB [auth p]151Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AWB [auth q]137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15XB [auth r]142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AYB [auth s]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AZB [auth t]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AAC [auth u]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-ABC [auth v]144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20CC [auth w]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-ADC [auth x]87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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