4L3B

X-ray structure of the HRV2 A particle uncoating intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.5 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.309 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle.

Pickl-Herk, A.Luque, D.Vives-Adrian, L.Querol-Audi, J.Garriga, D.Trus, B.L.Verdaguer, N.Blaas, D.Caston, J.R.

(2013) Proc.Natl.Acad.Sci.USA 110: 20063-20068

  • DOI: 10.1073/pnas.1312128110

  • PubMed Abstract: 
  • During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-part ...

    During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress.


    Organizational Affiliation

    Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, A-1030 Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein VP1
A
289Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein VP2
B
261Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein VP3
C
237Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.5 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.309 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 311.930α = 90.00
b = 357.830β = 90.00
c = 386.670γ = 90.00
Software Package:
Software NamePurpose
DMphasing
DNAdata collection
SCALAdata scaling
MOSFLMdata reduction
DMmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary