6T4Q

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.15252/embj.2019103365
  • Primary Citation of Related Structures:  
    6T4Q, 6T7I, 6T7T, 6T83

  • 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. 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

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AB [auth SB]232Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15C [auth SP]117Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth SC]216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth SD]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AF [auth SE]258Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pG [auth SF]206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AH [auth SG]228Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AI [auth SH]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AJ [auth SI]198Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AK [auth SJ]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AL [auth SK]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AM [auth SL]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12N [auth SM]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13O [auth SN]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BP [auth SO]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AQ [auth SQ]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AR [auth SR]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AS [auth SS]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AT [auth ST]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20U [auth SU]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AV [auth SV]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AW [auth SW]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AX [auth SX]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AY [auth SY]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AZ [auth SZ]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-BAA [auth Sa]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-ABA [auth Sb]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-ACA [auth Sd]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-ADA [auth Se]60Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31EA [auth Sf]73Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinFA [auth Sg]312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AGA [auth Sc]63Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AJA [auth LA]251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3KA [auth LB]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-ALA [auth LC]361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5MA [auth LD]294Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-BNA [auth LE]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AOA [auth LF]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-APA [auth LG]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AQA [auth LH]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10RA [auth LI]218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BSA [auth LJ]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-ATA [auth LL]193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AUA [auth LM]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AVA [auth LN]203Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AWA [auth LO]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AXA [auth LP]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AYA [auth LQ]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AZA [auth LR]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AAB [auth LS]171Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ABB [auth LT]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-ACB [auth LU]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-ADB [auth LV]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AEB [auth LW]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25FB [auth LX]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AGB [auth LY]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AHB [auth LZ]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28IB [auth La]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth Lb]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30KB [auth Lc]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ALB [auth Ld]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32MB [auth Le]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-ANB [auth Lf]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AOB [auth Lg]112Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-APB [auth Lh]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AQB [auth Li]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ARB [auth Lj]85Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38SB [auth Lk]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39TB [auth Ll]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40UB [auth Lm]52Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AVB [auth Ln]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AWB [auth Lo]103Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AXB [auth Lp]91Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
nascent chainCC [auth 8]6Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-ADC [auth SA]206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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