6TNU

Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

The Ccr4-Not complex monitors the translating ribosome for codon optimality.

Buschauer, R.Matsuo, Y.Sugiyama, T.Chen, Y.H.Alhusaini, N.Sweet, T.Ikeuchi, K.Cheng, J.Matsuki, Y.Nobuta, R.Gilmozzi, A.Berninghausen, O.Tesina, P.Becker, T.Coller, J.Inada, T.Beckmann, R.

(2020) Science 368

  • DOI: 10.1126/science.aay6912
  • Primary Citation of Related Structures:  
    6TB3, 6TNU

  • PubMed Abstract: 
  • Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality ...

    Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de toshifumi.inada.a3@tohoku.ac.jp jmc71@case.edu.



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Entity ID: 3
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40S ribosomal protein S0-AC [auth P]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AD [auth Q]232Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15E117Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2F [auth R]216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3G [auth A]222Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AH [auth S]258Saccharomyces cerevisiaeMutation(s): 0 
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Rps5pI [auth B]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AJ [auth T]228Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AK [auth U]184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8L [auth V]187Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AM [auth W]184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AN [auth C]92Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AO [auth X]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12P [auth D]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13Q [auth Y]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-BR [auth Z]127Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AS [auth F]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-BT [auth G]125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AU [auth H]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AV [auth I]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20W [auth J]100Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AY [auth a]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AZ [auth b]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AAA [auth c]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-ABA [auth d]134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-ACA [auth K]82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-BDA [auth e]97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-AEA [auth f]81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-AFA [auth M]53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AGA [auth g]60Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31HA [auth N]73Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinIA [auth O]312Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-AJA [auth L]63Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AOA [auth AW]251Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3PA [auth BA]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AQA [auth BE]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5RA [auth BI]294Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-BSA [auth BM]175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-ATA [auth BO]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AUA [auth AA]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AVA [auth AD]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10WA [auth BD]218Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BXA [auth AG]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AYA [auth AJ]193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AZA [auth AM]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AAB [auth AQ]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-ABB [auth AU]197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-ACB [auth AX]183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-ADB [auth BB]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AEB [auth BF]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AFB [auth BH]171Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AGB [auth BJ]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AHB [auth BL]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AIB [auth AB]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AJB [auth AE]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25KB [auth AH]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-ALB [auth AK]125Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AMB [auth AN]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28NB [auth AR]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L29OB [auth AV]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L30PB [auth AY]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L31-AQB [auth BC]109Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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60S ribosomal protein L32RB [auth BG]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L33-ASB [auth BK]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L34-ATB [auth BN]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L35-AUB [auth BP]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L36-AVB [auth AC]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L37-AWB [auth AF]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L38XB [auth AI]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L39YB [auth AL]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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Ubiquitin-60S ribosomal protein L40ZB [auth AO]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L41-AAC [auth AS]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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60S ribosomal protein L42-ABC [auth AP]103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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60S ribosomal protein L43-ACC [auth AT]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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Eukaryotic translation initiation factor 5A-1DC [auth eI]154Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
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60S ribosomal protein L1EC [auth BT]210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S rRNAA [auth 2]1798Saccharomyces cerevisiae
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  • Entity ID: 2
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    mRNAB [auth l]6Saccharomyces cerevisiae
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    Entity ID: 24
    MoleculeChainsLengthOrganismImage
    P-site tRNAX [auth n]75Saccharomyces cerevisiae
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    Entity ID: 37
    MoleculeChainsLengthOrganismImage
    A-site tRNAKA [auth m]76Saccharomyces cerevisiae
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    Entity ID: 38
    MoleculeChainsLengthOrganismImage
    25S rRNALA [auth BQ]3184Saccharomyces cerevisiae
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    Entity ID: 39
    MoleculeChainsLengthOrganismImage
    5S rRNAMA [auth BR]121Saccharomyces cerevisiae
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    Entity ID: 40
    MoleculeChainsLengthOrganismImage
    5.8S rRNANA [auth BS]158Saccharomyces cerevisiae
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    Small Molecules
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    5CT
    Query on 5CT
    DC [auth eI]PEPTIDE LINKINGC10 H23 N3 O3LYS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.10 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 Foundation (DFG)GermanyBE1814/15-1

    Revision History  (Full details and data files)

    • Version 1.0: 2020-04-22
      Type: Initial release
    • Version 1.1: 2020-04-29
      Changes: Database references