6Q8Y

Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex


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 1.3 of the entry. See complete history


Literature

Structure of the 80S ribosome-Xrn1 nuclease complex.

Tesina, P.Heckel, E.Cheng, J.Fromont-Racine, M.Buschauer, R.Kater, L.Beatrix, B.Berninghausen, O.Jacquier, A.Becker, T.Beckmann, R.

(2019) Nat Struct Mol Biol 26: 275-280

  • DOI: 10.1038/s41594-019-0202-5
  • Primary Citation of Related Structures:  
    6Q8Y

  • PubMed Abstract: 
  • Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved 5'-to-3' exoribonuclease Xrn1 has a crucial role in eukaryotic mRNA homeostasis by degrading decapped or cleaved mRNAs post-translationally and, more surprisingly, also co-translationally ...

    Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved 5'-to-3' exoribonuclease Xrn1 has a crucial role in eukaryotic mRNA homeostasis by degrading decapped or cleaved mRNAs post-translationally and, more surprisingly, also co-translationally. Here we report that active Xrn1 can directly and specifically interact with the translation machinery. A cryo-electron microscopy structure of a programmed Saccharomyces cerevisiae 80S ribosome-Xrn1 nuclease complex reveals how the conserved core of Xrn1 enables binding at the mRNA exit site of the ribosome. This interface provides a conduit for channelling of the mRNA from the ribosomal decoding site directly into the active center of the nuclease, thus separating mRNA decoding from degradation by only 17 ± 1 nucleotides. These findings explain how rapid 5'-to-3' mRNA degradation is coupled efficiently to its final round of mRNA translation.


    Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.



Macromolecules

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Entity ID: 2
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60S ribosomal protein L8-A AA233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-A AB136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-A AC100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A AD191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A AE67Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-A AF87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-B AG169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 AH121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38 AI77Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-A AJ193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A AK126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39 AL50Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-A AM136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-A AN135Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40 AO52Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-A AP105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A AQ203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 AR148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-B AS25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-A AT91Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A AU197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29 AV58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-A AW252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A AX183Saccharomyces 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 d132Saccharomyces 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 S30-A g60Saccharomyces cerevisiaeMutation(s): 0 
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5'-3' exoribonuclease 1 z916Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13
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60S ribosomal protein L30 AY97Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 BA386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-A BB185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-A BC109Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 BD220Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-A BE361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A BF188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32 BG127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A BH172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 BI296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A BJ159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-A BK106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-A BL100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-A BM175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-A BN112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-A BO222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-A BP119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 A223Saccharomyces cerevisiaeMutation(s): 0 
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Rps5p B206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-A C96Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12 D121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 E121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-A F141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-A G125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-A H139Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20 J107Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-A K70Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-A L63Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-A M53Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31 N51Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein O318Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
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40S ribosomal protein S0-A P219Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
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40S ribosomal protein S1-A Q214Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
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40S ribosomal protein S2 R220Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
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40S ribosomal protein S4-A S260Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
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40S ribosomal protein S6-A T226Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S7-A U184Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
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40S ribosomal protein S8-A V199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S9-A W178Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
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40S ribosomal protein S11-A X155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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40S ribosomal protein S13 Y150Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 81
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40S ribosomal protein S14-B Z127Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 82
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40S ribosomal protein S19-A I143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
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18S ribosomal RNA21797Saccharomyces cerevisiae
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  • Entity ID: 34
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    mRNAl17Saccharomyces cerevisiae
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    Entity ID: 35
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    P-site tRNAn76Saccharomyces cerevisiae
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    Entity ID: 36
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    E-site tRNAm75Saccharomyces cerevisiae
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    Entity ID: 54
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    25S ribosomal RNABQ3396Saccharomyces cerevisiae
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    Entity ID: 55
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    5S ribosomal RNABR121Saccharomyces cerevisiae
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    Entity ID: 56
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    5.8S ribosomal RNABS158Saccharomyces cerevisiae
    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 FoundationGermanyFOR1805
    German Research FoundationGermanyBE1814/15-1

    Revision History  (Full details and data files)

    • Version 1.0: 2019-03-13
      Type: Initial release
    • Version 1.1: 2019-04-03
      Changes: Data collection, Database references
    • Version 1.2: 2019-04-17
      Changes: Data collection, Database references
    • Version 1.3: 2019-12-18
      Changes: Data collection, Other