6T7I

Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts.

Tesina, P.Lessen, L.N.Buschauer, R.Cheng, J.Wu, C.C.Berninghausen, O.Buskirk, A.R.Becker, T.Beckmann, R.Green, R.

(2020) EMBO J 39: e103365-e103365

  • DOI: 10.15252/embj.2019103365
  • Primary Citation of Related Structures:  
    6T4Q, 6T83, 6T7T, 6T7I

  • PubMed Abstract: 
  • Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls ...

    Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.


    Organizational Affiliation

    Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.



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40S ribosomal protein S0-AB [auth SA]252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AC [auth SB]255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15D [auth SP]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2E [auth SC]254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3F [auth SD]240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AG [auth SE]261Saccharomyces cerevisiaeMutation(s): 0 
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Rps5pH [auth SF]225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AI [auth SG]236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AJ [auth SH]190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AK [auth SI]200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AL [auth SJ]197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AM [auth SK]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AN [auth SL]156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12O [auth SM]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13P [auth SN]151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-AQ [auth SO]137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AR [auth SQ]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-BS [auth SR]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AT [auth SS]146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AU [auth ST]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20V [auth SU]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AW [auth SV]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AX [auth SW]130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AY [auth SX]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AZ [auth SY]135Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-AAA [auth SZ]108Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-ABA [auth Sa]119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ACA [auth Sb]82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-ADA [auth Sd]56Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AEA [auth Se]63Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31FA [auth Sf]152Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinGA [auth Sg]319Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-BHA [auth Sc]67Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AKA [auth LA]254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3LA [auth LB]387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AMA [auth LC]362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5NA [auth LD]297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-BOA [auth LE]176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-APA [auth LF]244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AQA [auth LG]256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-ARA [auth LH]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10SA [auth LI]221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-ATA [auth LJ]174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AUA [auth LL]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AVA [auth LM]138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AWA [auth LN]204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AXA [auth LO]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AYA [auth LP]184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AZA [auth LQ]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AAB [auth LR]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-ABB [auth LS]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-ACB [auth LT]160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-ADB [auth LU]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AEB [auth LV]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-BFB [auth LW]155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25GB [auth LX]142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AHB [auth LY]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AIB [auth LZ]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28JB [auth La]149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L29KB [auth Lb]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein L30LB [auth Lc]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L31-AMB [auth Ld]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L32NB [auth Le]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L33-AOB [auth Lf]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L34-APB [auth Lg]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L35-AQB [auth Lh]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L36-ARB [auth Li]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L37-ASB [auth Lj]88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L38TB [auth Lk]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L39UB [auth Ll]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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Ubiquitin-60S ribosomal protein L40VB [auth Lm]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L41-BWB [auth Ln]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L42-AXB [auth Lo]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L43-AYB [auth Lp]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S ribosomal RNAA [auth C2]1800Saccharomyces cerevisiae
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Entity ID: 35
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5S ribosomal RNAIA [auth C4]121Saccharomyces cerevisiae
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Entity ID: 36
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5.8S ribosomal RNAJA [auth C3]158Saccharomyces cerevisiae
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Entity ID: 78
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25S ribosomal RNAZB [auth C1]3396Saccharomyces cerevisiae
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  • Entity ID: 79
    MoleculeChainsLengthOrganismImage
    mRNAAC [auth 5]18Saccharomyces cerevisiae
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    Entity ID: 80
    MoleculeChainsLengthOrganismImage
    ICG tRNA ArgBC [auth 6]76Saccharomyces cerevisiae
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    Entity ID: 81
    MoleculeChainsLengthOrganismImage
    tRNA (E-site)CC [auth 7]75Saccharomyces cerevisiae
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    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.20 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermanyBE1814/15-1

    Revision History  (Full details and data files)

    • Version 1.0: 2019-12-25
      Type: Initial release
    • Version 1.1: 2020-01-01
      Changes: Database references
    • Version 1.2: 2020-02-12
      Changes: Database references