4D61

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 SAB [auth A]295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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40S RIBOSOMAL PROTEIN S3AC [auth B]264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 4
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40S RIBOSOMAL PROTEIN S2D [auth C]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
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40S RIBOSOMAL PROTEIN S3E [auth D]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1F [auth E]263Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S5G [auth F]204Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S6H [auth G]249Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S7I [auth H]194Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S8J [auth I]208Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S9K [auth J]194Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S10L [auth K]165Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S11M [auth L]158Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S12N [auth M]132Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S13O [auth N]151Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S14P [auth O]151Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S15Q [auth P]145Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S16R [auth Q]146Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S17S [auth R]135Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S18T [auth S]152Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S19U [auth T]145Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S20V [auth U]119Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S21W [auth V]83Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S15AX [auth W]130Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S23Y [auth X]143Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S24Z [auth Y]133Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S25AA [auth Z]125Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S26BA [auth a]115Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S27CA [auth b]84Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S28DA [auth c]69Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S29EA [auth d]56Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN S30FA [auth e]59Oryctolagus cuniculusMutation(s): 0 
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UBIQUITIN-40S RIBOSOMAL PROTEIN S27AGA [auth f]156Oryctolagus cuniculusMutation(s): 0 
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GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1HA [auth g]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1IA [auth h]436Homo sapiensMutation(s): 0 
Gene Names: ETF1ERF1RF1SUP45L1
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EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3AJA [auth i]426Homo sapiensMutation(s): 0 
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18S RRNAA [auth 1]1869Oryctolagus cuniculus
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CRICKET PARALYSIS VIRUS IRES RNAKA [auth j]201Cricket paralysis virus
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: 2015-03-04
    Type: Initial release
  • Version 2.0: 2017-08-30
    Changes: Atomic model, Data collection, Derived calculations, Structure summary