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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AB [auth AA]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AC [auth AB]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AD [auth AC]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AE [auth AD]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AF [auth AE]67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AG [auth AF]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BH [auth AG]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25I [auth AH]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38J [auth AI]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AK [auth AJ]193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AL [auth AK]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39M [auth AL]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AN [auth AM]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AO [auth AN]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40P [auth AO]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AQ [auth AP]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AR [auth AQ]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28S [auth AR]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-BT [auth AS]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AU [auth AT]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AV [auth AU]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29W [auth AV]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AX [auth AW]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AY [auth AX]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AZ [auth a]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AAA [auth b]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ABA [auth c]144Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-ACA [auth d]132Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-BDA [auth e]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AEA [auth f]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AFA [auth g]60Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
5'-3' exoribonuclease 1GA [auth z]916Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30KA [auth AY]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3LA [auth BA]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AMA [auth BB]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ANA [auth BC]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10OA [auth BD]220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-APA [auth BE]361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AQA [auth BF]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32RA [auth BG]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-ASA [auth BH]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5TA [auth BI]296Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AUA [auth BJ]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AVA [auth BK]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AWA [auth BL]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AXA [auth BM]175Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AYA [auth BN]112Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AZA [auth BO]222Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AAB [auth BP]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3EB [auth A]223Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pFB [auth B]206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AGB [auth C]96Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12HB [auth D]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15IB [auth E]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AJB [auth F]141Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AKB [auth G]125Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-ALB [auth H]139Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20MB [auth J]107Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-ANB [auth K]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AOB [auth L]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-APB [auth M]53Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31QB [auth N]51Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinRB [auth O]318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-ASB [auth P]219Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-ATB [auth Q]214Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2UB [auth R]220Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AVB [auth S]260Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AWB [auth T]226Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AXB [auth U]184Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AYB [auth V]199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AZB [auth W]178Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AAC [auth X]155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13BC [auth Y]150Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BCC [auth Z]127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-ADC [auth I]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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