4D5L

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires.

Muhs, M.Hilal, T.Mielke, T.Skabkin, M.A.Sanbonmatsu, K.Y.Pestova, T.V.Spahn, C.M.T.

(2015) Mol Cell 57: 422

  • DOI: 10.1016/j.molcel.2014.12.016
  • Primary Citation of Related Structures:  
    4D67, 4D5Y, 4D5N, 4D61, 4D5L

  • PubMed Abstract: 
  • The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site ...

    The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site. Here, we present cryoelectron microscopy (cryo-EM) maps of 80S⋅CrPV-STOP ⋅ eRF1 ⋅ eRF3 ⋅ GMPPNP and 80S⋅CrPV-STOP ⋅ eRF1 complexes, revealing a previously unseen binding state of the IRES and directly rationalizing that an eEF2-dependent translocation of the IRES is required to allow the first A-site occupation. During this unusual translocation event, the IRES undergoes a pronounced conformational change to a more stretched conformation. At the same time, our structural analysis provides information about the binding modes of eRF1 ⋅ eRF3 ⋅ GMPPNP and eRF1 in a minimal system. It shows that neither eRF3 nor ABCE1 are required for the active conformation of eRF1 at the intersection between eukaryotic termination and recycling.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: christian.spahn@charite.de.



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Entity ID: 2
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40S RIBOSOMAL PROTEIN ES26 A295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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40S RIBOSOMAL PROTEIN ES27 B264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 4
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40S RIBOSOMAL PROTEIN ES28 C293Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US14 D243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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40S RIBOSOMAL PROTEIN ES30 E263Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES31 F204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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40S RIBOSOMAL PROTEIN RACK1 G249Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES7 H194Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES8 I208Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US4 J194Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES10 K165Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US17 L158Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES12 M132Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US15 N151Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US19 P145Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US13 S152Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES19 T145Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US10 U119Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES21 V83Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US8 W130Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US12 X142Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES24 Y133Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES25 Z125Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US2 a115Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES1 b84Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US5 c69Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US3 d56Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES4 e59Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN US7 f156Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES6 g317Oryctolagus cuniculusMutation(s): 0 
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18S RRNA 211869Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 2.0: 2017-08-23
    Changes: Atomic model, Data collection, Derived calculations