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: 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L8A257Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L3B403Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L4C427Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L5D297Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L6E288Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7F248Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7AG266Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9H192Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10I214Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11J178Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13K [auth L]211Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L14L [auth M]215Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L15M [auth N]204Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13AN [auth O]203Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L17O [auth P]184Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18P [auth Q]188Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L19Q [auth R]196Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18AR [auth S]176Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L21S [auth T]160Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L22T [auth U]128Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23U [auth V]140Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23AW [auth X]156Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L26X [auth Y]145Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27Y [auth Z]136Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27AZ [auth a]148Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29AA [auth b]159Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30BA [auth c]115Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L31CA [auth d]125Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L32DA [auth e]135Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35AEA [auth f]110Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L34FA [auth g]117Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35GA [auth h]123Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36HA [auth i]105Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37IA [auth j]97Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L38JA [auth k]70Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40LA [auth m]128Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L41MA [auth n]25Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36ANA [auth o]106Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37AOA [auth p]92Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L28PA [auth t]137Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10AQA [auth u]210Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 44
MoleculeChainsLengthOrganismImage
28S RRNARA [auth 2]5025Oryctolagus cuniculus
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 45
MoleculeChainsLengthOrganismImage
5.8S RRNASA [auth 3]194Oryctolagus cuniculus
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 46
MoleculeChainsLengthOrganismImage
5S RRNATA [auth 4]121Oryctolagus 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 2.0: 2017-08-23
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-10-23
    Changes: Data collection, Other