Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 113.40 kDa 
• Atom Count: 7707 
• Residue Count: 637 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4D5N

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

• DOI: 10.2210/pdb4D5N/pdb
• EMDataResource: EMD-2810

• Classification: RIBOSOME/RNA
• Organism(s): Homo sapiens, Cricket paralysis virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-06 Released: 2015-02-04 
• Deposition Author(s): Muhs, M., Hilal, T., Mielke, T., Skabkin, M.A., Sanbonmatsu, K.Y., Pestova, T.V., Spahn, C.M.T.

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Experimental Data Snapshot

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

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

• PubMed: 25601755 
• 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. 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.

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Organizational Affiliation: 

Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1	A	436	Homo sapiens	Mutation(s): 0  Gene Names: ETF1, ERF1, RF1, SUP45L1
Find proteins for P62495 (Homo sapiens) Explore P62495  Go to UniProtKB:  P62495
NIH Common Fund Data Resources
PHAROS  P62495 GTEx  ENSG00000120705

Entity ID: 2
Molecule	Chains	Length	Organism	Image
CRICKET PARALYSIS VIRUS IRES RNA	X	201	Cricket paralysis virus

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-06 
• Released Date: 2015-02-04 
Deposition Author(s): Muhs, M., Hilal, T., Mielke, T., Skabkin, M.A., Sanbonmatsu, K.Y., Pestova, T.V., Spahn, C.M.T.

Revision History 

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 2.0: 2017-08-30
  Changes: Atomic model, Data collection, Derived calculations