6T83

Structure of yeast disome (di-ribosome) stalled on poly(A) tract.


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 1.2 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 Ab], CC [auth b]252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AC [auth Ba], DC [auth c]255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15D [auth Pb], RC [auth q]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2E [auth Cb], EC [auth d]254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3F [auth Db], FC [auth e]240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AG [auth Eb], GC [auth f]261Saccharomyces cerevisiaeMutation(s): 0 
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Rps5pH [auth Fb], HC [auth g]225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AI [auth Gb], IC [auth h]236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AJ [auth Hb], JC [auth i]190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AK [auth Ib], KC [auth j]200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AL [auth Jb], LC [auth k]197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AM [auth Kb], MC [auth l]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AN [auth Lb], NC [auth m]156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12O [auth Mb], OC [auth n]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13P [auth Nb], PC [auth o]151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-AQ [auth Ob], QC [auth p]137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AR [auth Qb], SC [auth r]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-BS [auth Rb], TC [auth s]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AT [auth Sb], UC [auth t]146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AU [auth Tb], VC [auth u]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20V [auth Ub], WC [auth v]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AW [auth Vb], XC [auth w]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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40S ribosomal protein S22-AX [auth Wb], YC [auth x]130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AY [auth Xb], ZC [auth y]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AZ [auth Yb], AD [auth z]135Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-ABD [auth 0], AA [auth Zb]108Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-ACD [auth 1], BA [auth ab]119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ADD [auth 2], CA [auth bb]82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-AFD [auth 4], DA [auth db]56Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AGD [auth 5], EA [auth eb]63Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31HD [auth 6], FA [auth fb]152Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinID [auth 7], GA [auth gb]319Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-BED [auth 3], HA [auth cb]67Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AKA [auth Ay], MD [auth Da]254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3LA [auth By], ND [auth Ea]387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AMA [auth Cy], OD [auth Fa]362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5NA [auth Dy], PD [auth Ga]297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AOA [auth Ey], QD [auth Ha]176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-APA [auth Fy], RD [auth Ia]244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AQA [auth Gy], SD [auth Ja]256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-ARA [auth Hy], TD [auth Ka]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10SA [auth Iy], UD [auth La]221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-ATA [auth Jy], VD [auth Ma]174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AUA [auth Ly], WD [auth Na]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AVA [auth My], XD [auth Oa]138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AWA [auth Ny], YD [auth Pa]204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AXA [auth Oy], ZD [auth Qa]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AAE [auth A], YA [auth Py]184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-ABE [auth B], ZA [auth Qy]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-ACE [auth C], AB [auth Ry]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-ADE [auth D], BB [auth Sy]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AEE [auth E], CB [auth Ty]160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AFE [auth F], DB [auth Uy]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AGE [auth G], EB [auth Vy]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AHE [auth H], FB [auth Wy]155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25IE [auth I], GB [auth Xy]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-AJE [auth J], HB [auth Yy]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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60S ribosomal protein L27-AKE [auth K], IB [auth Zy]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28LE [auth L], JB [auth ay]149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29ME [auth M], KB [auth by]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein L30NE [auth N], LB [auth cy]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L31-AOE [auth O], MB [auth dy]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32PE [auth P], NB [auth ey]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-AQE [auth Q], OB [auth fy]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-ARE [auth R], PB [auth gy]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-ASE [auth S], QB [auth hb]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-ATE [auth T], RB [auth ib]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-AUE [auth U], SB [auth jb]88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38VE [auth V], TB [auth kb]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39WE [auth W], UB [auth lb]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40XE [auth X], VB [auth mb]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-AYE [auth Y], WB [auth nb]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L42-AZE [auth Z], XB [auth ob]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L43-AAF [auth aa], YB [auth pb]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0BF [auth ba]311Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S rRNAA [auth 2b], BC [auth a]1800Saccharomyces cerevisiae
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Entity ID: 35
MoleculeChainsLengthOrganismImage
5S rRNAIA [auth 4b], KD [auth Bb]121Saccharomyces cerevisiae
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Entity ID: 36
MoleculeChainsLengthOrganismImage
5.8S rRNAJA [auth 3b], LD [auth Ca]158Saccharomyces cerevisiae
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Entity ID: 78
MoleculeChainsLengthOrganismImage
25S rRNAZB [auth 1b], JD [auth Aa]3396Saccharomyces cerevisiae
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Entity ID: 79
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tRNAAC [auth 6b], CF [auth 8]76Saccharomyces cerevisiae
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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



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