3J6Y

S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center.

Koh, C.S.Brilot, A.F.Grigorieff, N.Korostelev, A.A.

(2014) Proc Natl Acad Sci U S A 111: 9139-9144

  • DOI: 10.1073/pnas.1406335111
  • Primary Citation of Related Structures:  
    3J6X, 3J6Y

  • PubMed Abstract: 
  • In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner ...

    In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA-like structure in the A site, whereas the 40S P site remains unoccupied during this initial step.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605; andrei.korostelev@umassmed.edu niko@grigorieff.org.



Macromolecules

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Entity ID: 4
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60S ribosomal protein L1D [auth L1]217Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L2E [auth L2]254Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L3F [auth L3]387Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 7
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60S ribosomal protein L4G [auth L4]362Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L5H [auth L5]297Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 9
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60S ribosomal protein L6I [auth L6]176Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 10
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60S ribosomal protein L7J [auth L7]244Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L8K [auth L8]256Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L9L [auth L9]191Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L10M [auth 50]221Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L11N [auth 51]174Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L13O [auth 53]199Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L14P [auth 54]138Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L15Q [auth 55]204Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L16R [auth 56]199Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L17S [auth 57]184Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L18T [auth 58]186Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L19U [auth 59]189Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L20V [auth 60]172Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 23
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60S ribosomal protein L21W [auth 61]160Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L22X [auth 62]121Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L23Y [auth 63]137Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 26
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60S ribosomal protein L24Z [auth 64]155Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L25AA [auth 65]142Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L26BA [auth 66]127Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 29
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60S ribosomal protein L27CA [auth 67]136Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L28DA [auth 68]149Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L29EA [auth 69]59Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L30FA [auth 70]105Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L31GA [auth 71]113Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L32HA [auth 72]130Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L33IA [auth 73]107Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L34JA [auth 74]121Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 37
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60S ribosomal protein L35KA [auth 75]120Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L36LA [auth 76]100Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L37MA [auth 77]88Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L38NA [auth 78]78Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L39OA [auth 79]51Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L40PA [auth 80]128Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L41QA [auth 81]25Saccharomyces cerevisiae W303Mutation(s): 0 
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60S ribosomal protein L42RA [auth 82]106Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L43SA [auth 83]92Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S0UA [auth S0]252Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S1VA [auth S1]255Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S2WA [auth S2]254Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S3XA [auth S3]240Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 51
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40S ribosomal protein S4YA [auth S4]261Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S5ZA [auth S5]225Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S6AB [auth S6]236Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S7BB [auth S7]190Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S8CB [auth S8]200Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S9DB [auth S9]197Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 57
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40S ribosomal protein S10EB [auth 10]105Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S11FB [auth 11]156Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S12GB [auth 12]143Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S13HB [auth 13]151Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S14IB [auth 14]137Saccharomyces cerevisiae W303Mutation(s): 0 
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40S ribosomal protein S15JB [auth 15]142Saccharomyces cerevisiae W303Mutation(s): 0 
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Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
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40S ribosomal protein S16KB [auth 16]143Saccharomyces cerevisiae W303Mutation(s): 0 
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Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
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40S ribosomal protein S17LB [auth 17]136Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S18MB [auth 18]146Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S19NB [auth 19]144Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S20OB [auth 20]121Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S21PB [auth 21]87Saccharomyces cerevisiae W303Mutation(s): 0 
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Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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40S ribosomal protein S22QB [auth 22]130Saccharomyces cerevisiae W303Mutation(s): 0 
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Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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40S ribosomal protein S23RB [auth 23]145Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S24SB [auth 24]135Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S25TB [auth 25]108Saccharomyces cerevisiae W303Mutation(s): 0 
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Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
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40S ribosomal protein S26UB [auth 26]119Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S27VB [auth 27]82Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S28WB [auth 28]67Saccharomyces cerevisiae W303Mutation(s): 0 
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Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
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40S ribosomal protein S29XB [auth 29]56Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S30YB [auth 30]63Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S31ZB [auth 31]152Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 79
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Guanine nucleotide-binding protein subunit beta-like proteinAC [auth RA]319Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 1
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25S ribosomal RNAA [auth 2S]3395Saccharomyces cerevisiae W303
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Entity ID: 2
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5.8S ribosomal RNAB [auth 8S]158Saccharomyces cerevisiae W303
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Entity ID: 3
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5S ribosomal RNAC [auth 5S]121Saccharomyces cerevisiae W303
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Entity ID: 46
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18S ribosomal RNATA [auth 1S]1798Saccharomyces cerevisiae W303
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Entity ID: 80
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TSV IRES mRNABC [auth IR]201Taura syndrome virus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Other
  • Version 1.3: 2014-12-17
    Changes: Other
  • Version 1.4: 2018-07-18
    Changes: Data collection