4D5Y

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 2.2 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: 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.



Macromolecules

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Entity ID: 1
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60S RIBOSOMAL PROTEIN UL2A257Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
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60S RIBOSOMAL PROTEIN UL3B403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
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60S RIBOSOMAL PROTEIN UL4C427Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
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60S RIBOSOMAL PROTEIN UL18D297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
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60S RIBOSOMAL PROTEIN EL6E288Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
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60S RIBOSOMAL PROTEIN UL30F248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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60S RIBOSOMAL PROTEIN EL8G266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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60S RIBOSOMAL PROTEIN UL6H192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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60S RIBOSOMAL PROTEIN UL16I214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
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60S RIBOSOMAL PROTEIN UL5J178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
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60S RIBOSOMAL PROTEIN EL13K [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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60S RIBOSOMAL PROTEIN EL14L [auth M]215Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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60S RIBOSOMAL PROTEIN EL15M [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
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60S RIBOSOMAL PROTEIN UL13N [auth O]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
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60S RIBOSOMAL PROTEIN UL22O [auth P]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
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60S RIBOSOMAL PROTEIN EL18P [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
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60S RIBOSOMAL PROTEIN UL19Q [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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60S RIBOSOMAL PROTEIN EL20R [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
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60S RIBOSOMAL PROTEIN EL21S [auth T]160Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL22T [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
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60S RIBOSOMAL PROTEIN UL14U [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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60S RIBOSOMAL PROTEIN EL24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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60S RIBOSOMAL PROTEIN UL23W [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
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60S RIBOSOMAL PROTEIN UL24X [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
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60S RIBOSOMAL PROTEIN EL27Y [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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60S RIBOSOMAL PROTEIN UL15Z [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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60S RIBOSOMAL PROTEIN EL29AA [auth b]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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60S RIBOSOMAL PROTEIN EL30BA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
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60S RIBOSOMAL PROTEIN EL31CA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
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60S RIBOSOMAL PROTEIN EL32DA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
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60S RIBOSOMAL PROTEIN EL33EA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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60S RIBOSOMAL PROTEIN EL34FA [auth g]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S RIBOSOMAL PROTEIN UL29GA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
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60S RIBOSOMAL PROTEIN EL36HA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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60S RIBOSOMAL PROTEIN EL37IA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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60S RIBOSOMAL PROTEIN EL38JA [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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60S RIBOSOMAL PROTEIN EL39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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60S RIBOSOMAL PROTEIN EL40LA [auth m]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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60S RIBOSOMAL PROTEIN EL41MA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
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60S RIBOSOMAL PROTEIN EL44NA [auth o]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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60S RIBOSOMAL PROTEIN EL43OA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
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60S RIBOSOMAL PROTEIN EL28PA [auth t]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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60S RIBOSOMAL PROTEIN UL1QA [auth u]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsLengthOrganismImage
28S Ribosomal RNARA [auth 2]5025Oryctolagus cuniculus
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Entity ID: 45
MoleculeChainsLengthOrganismImage
5.8S Ribosomal RNASA [auth 3]194Oryctolagus cuniculus
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Entity ID: 46
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5S Ribosomal RNATA [auth 4]119Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 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: 2015-03-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Source and taxonomy
  • Version 2.0: 2017-08-23
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-10-30
    Changes: Data collection, Derived calculations
  • Version 2.2: 2019-12-18
    Changes: Other