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:  
    6TNU, 6TB3

  • 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.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-A P206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-A Q232Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 E117Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 R216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 A222Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-A S258Saccharomyces cerevisiaeMutation(s): 0 
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Rps5p B206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-A T228Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-A U184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8 V187Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-A W184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-A C92Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-A X142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12 D121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 Y150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-B Z127Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-A F141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-B G125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-A H145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-A I143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20 J100Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-A a87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-A b129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-A c144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-A d134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-A K82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-B e97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-A f81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-A M53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-A g60Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31 N73Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein O312Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-A L63Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-A AW251Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 BA386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-A BE361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 BI294Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-B BM175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-A BO222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-A AA233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A AD191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 BD218Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-B AG169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-A AJ193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-A AM136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A AQ203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A AU197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A AX183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-A BB185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A BF188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A BH171Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A BJ159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L22-A BL100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-A AB136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A AE126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 AH121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A AK125Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-A AN135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 AR148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29 AV58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30 AY96Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-A BC109Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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60S ribosomal protein L32 BG127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L33-A BK106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L34-A BN112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L35-A BP119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L36-A AC99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L37-A AF81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L38 AI77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L39 AL50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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Ubiquitin-60S ribosomal protein L40 AO52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L41-A AS25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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60S ribosomal protein L42-A AP103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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60S ribosomal protein L43-A AT91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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Eukaryotic translation initiation factor 5A-1 eI154Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
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60S ribosomal protein L1 BT210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S rRNA21798Saccharomyces cerevisiae
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    • Entity ID: 2
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    mRNAl6Saccharomyces cerevisiae
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    Entity ID: 24
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    P-site tRNAn75Saccharomyces cerevisiae
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    Entity ID: 37
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    A-site tRNAm76Saccharomyces cerevisiae
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    Entity ID: 38
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    25S rRNABQ3184Saccharomyces cerevisiae
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    Entity ID: 39
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    5S rRNABR121Saccharomyces cerevisiae
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    Entity ID: 40
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    5.8S rRNABS158Saccharomyces cerevisiae
    Small Molecules
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    5CT
    Query on 5CT    		eIPEPTIDE 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

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    View more in-depth experimental data

    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