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.



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60S ribosomal protein L8-AB [auth AA]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AC [auth AB]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-AD [auth AC]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AE [auth AD]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AF [auth AE]67Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-AG [auth AF]87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BH [auth AG]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25I [auth AH]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38J [auth AI]77Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AK [auth AJ]193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AL [auth AK]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39M [auth AL]50Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AN [auth AM]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AO [auth AN]135Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40P [auth AO]52Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-AQ [auth AP]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AR [auth AQ]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28S [auth AR]148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-BT [auth AS]25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-AU [auth AT]91Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AV [auth AU]197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29W [auth AV]58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AX [auth AW]252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AY [auth AX]183Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AZ [auth a]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AAA [auth b]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-ABA [auth c]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-ACA [auth d]132Saccharomyces 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 S30-AFA [auth g]60Saccharomyces cerevisiaeMutation(s): 0 
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5'-3' exoribonuclease 1GA [auth z]916Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13
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60S ribosomal protein L30KA [auth AY]97Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3LA [auth BA]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AMA [auth BB]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-ANA [auth BC]109Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10OA [auth BD]220Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-APA [auth BE]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AQA [auth BF]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32RA [auth BG]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-ASA [auth BH]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5TA [auth BI]296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AUA [auth BJ]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-AVA [auth BK]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AWA [auth BL]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AXA [auth BM]175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-AYA [auth BN]112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AZA [auth BO]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-AAB [auth BP]119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3EB [auth A]223Saccharomyces cerevisiaeMutation(s): 0 
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Rps5pFB [auth B]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AGB [auth C]96Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12HB [auth D]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15IB [auth E]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AJB [auth F]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-AKB [auth G]125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-ALB [auth H]139Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20MB [auth J]107Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-ANB [auth K]70Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
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40S ribosomal protein S28-AOB [auth L]63Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
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40S ribosomal protein S29-APB [auth M]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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Ubiquitin-40S ribosomal protein S31QB [auth N]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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Guanine nucleotide-binding protein subunit beta-like proteinRB [auth O]318Saccharomyces cerevisiaeMutation(s): 0 
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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-ASB [auth P]219Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S1-ATB [auth Q]214Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S2UB [auth R]220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S4-AVB [auth S]260Saccharomyces cerevisiaeMutation(s): 0 
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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-AWB [auth T]226Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S7-AXB [auth U]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S8-AYB [auth V]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S9-AZB [auth W]178Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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40S ribosomal protein S11-AAC [auth X]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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40S ribosomal protein S13BC [auth Y]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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40S ribosomal protein S14-BCC [auth Z]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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40S ribosomal protein S19-ADC [auth I]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S ribosomal RNAA [auth 2]1797Saccharomyces cerevisiae
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  • Entity ID: 34
    MoleculeChainsLengthOrganismImage
    mRNAHA [auth l]17Saccharomyces cerevisiae
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    Entity ID: 35
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    P-site tRNAIA [auth n]76Saccharomyces cerevisiae
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    Entity ID: 36
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    E-site tRNAJA [auth m]75Saccharomyces cerevisiae
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    Entity ID: 54
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    25S ribosomal RNABB [auth BQ]3396Saccharomyces cerevisiae
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    Entity ID: 55
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    5S ribosomal RNACB [auth BR]121Saccharomyces cerevisiae
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    Entity ID: 56
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    5.8S ribosomal RNADB [auth BS]158Saccharomyces cerevisiae
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    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