4D67

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 2.1 of the entry. See complete history


Literature

Cryo-Em Structures of Ribosomal 80S Complexes with Termination Factors and Cricket Paralysis Virus Ires Reveal the Ires in the Translocated State

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

  • 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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L8257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L3403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L4427Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L5297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L6288Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7A266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9192Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10214Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11178Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13K [auth L]211Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L14L [auth M]215Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L15M [auth N]204Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L13AN [auth O]203Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L17O [auth P]184Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L18P [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L19Q [auth R]196Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18AR [auth S]176Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L21S [auth T]160Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L22T [auth U]128Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L23U [auth V]140Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L23AW [auth X]156Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L26X [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN L27Y [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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60S RIBOSOMAL PROTEIN L27AZ [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29AA [auth b]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30BA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L31CA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
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60S RIBOSOMAL PROTEIN L32DA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35AEA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L34FA [auth g]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S RIBOSOMAL PROTEIN L35GA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36HA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37IA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L38JA [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40LA [auth m]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L41MA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36ANA [auth o]106Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37AOA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L28PA [auth t]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10AQA [auth u]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains LengthOrganismImage
28S RRNARA [auth 2]5,025Oryctolagus cuniculus
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Entity ID: 45
MoleculeChains LengthOrganismImage
5.8S RRNASA [auth 3]194Oryctolagus cuniculus
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Entity ID: 46
MoleculeChains LengthOrganismImage
5S RRNATA [auth 4]121Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

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: 2017-08-23
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-10-23
    Changes: Data collection, Other