8RT1

BTV15 VP5 at pH 9.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

The effect of pH on the structure of Bluetongue virus VP5.

Zhang, H.El Omari, K.Sutton, G.Stuart, D.I.

(2024) J Gen Virol 105

  • DOI: https://doi.org/10.1099/jgv.0.002018
  • Primary Citation of Related Structures:  
    8RT0, 8RT1

  • PubMed Abstract: 

    The unenveloped Bluetongue virus capsid comprises several structural layers, the inner two comprising a core, which assembles before addition of the outer proteins, VP2 and VP5. Two symmetric trimers of VP5 fit like pegs into two distinct pits on the core and undergo pH conformational changes in the context of the virus, associated with cell entry. Here we show that in isolation VP5 alone undergoes essentially the same changes with pH and confirm a helical transition, indicating that VP5 is a motor during cell entry. In the absence of VP5 the two pits on the core differ from each other, presumably due to the asymmetric underlying structure of VP3, the innermost capsid protein. On insertion of VP5 these pits become closely similar and remain similar at low pH whilst VP5 is present. This natural asymmetry presumably destabilises the attachment of VP5, facilitating ejection upon low pH, membrane penetration and cell entry.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, Centre for Human Genetics, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP5
A, B, C, D, E
A, B, C, D, E, F, G, H, I
490Bluetongue virus 15Mutation(s): 0 
UniProt
Find proteins for R4J9Y2 (Bluetongue virus 15)
Explore R4J9Y2 
Go to UniProtKB:  R4J9Y2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4J9Y2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.399α = 119.54
b = 142.205β = 96.09
c = 142.151γ = 95.8
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomG1000099

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release