3TN9

X-ray structure of the HRV2 empty capsid (B-particle)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Insights into minor group rhinovirus uncoating: the X-ray structure of the HRV2 empty capsid.

Garriga, D.Pickl-Herk, A.Luque, D.Wruss, J.Caston, J.R.Blaas, D.Verdaguer, N.

(2012) Plos Pathog. 8: e1002473-e1002473

  • DOI: 10.1371/journal.ppat.1002473

  • PubMed Abstract: 
  • Upon attachment to their respective receptor, human rhinoviruses (HRVs) are internalized into the host cell via different pathways but undergo similar structural changes. This ultimately results in the delivery of the viral RNA into the cytoplasm for ...

    Upon attachment to their respective receptor, human rhinoviruses (HRVs) are internalized into the host cell via different pathways but undergo similar structural changes. This ultimately results in the delivery of the viral RNA into the cytoplasm for replication. To improve our understanding of the conformational modifications associated with the release of the viral genome, we have determined the X-ray structure at 3.0 Å resolution of the end-stage of HRV2 uncoating, the empty capsid. The structure shows important conformational changes in the capsid protomer. In particular, a hinge movement around the hydrophobic pocket of VP1 allows a coordinated shift of VP2 and VP3. This overall displacement forces a reorganization of the inter-protomer interfaces, resulting in a particle expansion and in the opening of new channels in the capsid core. These new breaches in the capsid, opening one at the base of the canyon and the second at the particle two-fold axes, might act as gates for the externalization of the VP1 N-terminus and the extrusion of the viral RNA, respectively. The structural comparison between native and empty HRV2 particles unveils a number of pH-sensitive amino acid residues, conserved in rhinoviruses, which participate in the structural rearrangements involved in the uncoating process.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein VP1
1
289Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein VP2
2
261Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein VP3
3
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: 3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.265 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 314.010α = 90.00
b = 356.850β = 90.00
c = 382.470γ = 90.00
Software Package:
Software NamePurpose
DMphasing
DNAdata collection
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release