3TN9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.265 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    3TN9

  • 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 replication ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP1 1289Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP2 2261Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP3 3237Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 314.01α = 90
b = 356.85β = 90
c = 382.47γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
DNAdata collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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