4PB6 | pdb_00004pb6

Feline calicivirus VP1 T=1 virus-like particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.00 Å
  • R-Value Free: 
    0.463 (Depositor), 0.448 (DCC) 
  • R-Value Work: 
    0.441 (Depositor), 0.426 (DCC) 
  • R-Value Observed: 
    0.442 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure determination of feline calicivirus virus-like particles in the context of a pseudo-octahedral arrangement.

Burmeister, W.P.Buisson, M.Estrozi, L.F.Schoehn, G.Billet, O.Hannas, Z.Sigoillot, C.Poulet, H.

(2015) PLoS One 10: e0119289-e0119289

  • DOI: https://doi.org/10.1371/journal.pone.0119289
  • Primary Citation Related Structures: 
    4PB6

  • PubMed Abstract: 

    The vesivirus feline calicivirus (FCV) is a positive strand RNA virus encapsidated by an icosahedral T=3 shell formed by the viral VP1 protein. Upon its expression in the insect cell - baculovirus system in the context of vaccine development, two types of virus-like particles (VLPs) were formed, a majority built of 60 subunits (T=1) and a minority probably built of 180 subunits (T=3). The structure of the small particles was determined by x-ray crystallography at 0.8 nm resolution helped by cryo-electron microscopy in order to understand their formation. Cubic crystals belonged to space group P213. Their self-rotation function showed the presence of an octahedral pseudo-symmetry similar to the one described previously by Agerbandje and co-workers for human parvovirus VLPs. The crystal structure could be solved starting from the published VP1 structure in the context of the T=3 viral capsid. In contrast to viral capsids, where the capsomers are interlocked by the exchange of the N-terminal arm (NTA) domain, this domain is disordered in the T=1 capsid of the VLPs. Furthermore it is prone to proteolytic cleavage. The relative orientation of P (protrusion) and S (shell) domains is alerted so as to fit VP1 to the smaller T=1 particle whereas the intermolecular contacts around 2-fold, 3-fold and 5-fold axes are conserved. By consequence the surface of the VLP is very similar compared to the viral capsid and suggests a similar antigenicity. The knowledge of the structure of the VLPs will help to improve their stability, in respect to a use for vaccination.


  • Organizational Affiliation
    • Unit of Virus Host Cell Interactions, Université Grenoble Alpes, Grenoble, France; Unit of Virus Host Cell Interactions, Unité Mixte Internationale 3265, Centre National de Recherche Scientifique, Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 1,185.95 kDa 
  • Atom Count: 77,840 
  • Modeled Residue Count: 10,040 
  • Deposited Residue Count: 10,900 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
545Feline calicivirusMutation(s): 0 
Gene Names: VP1
UniProt
Find proteins for A0A0J9X1Z3 (Feline calicivirus)
Explore A0A0J9X1Z3 
Go to UniProtKB:  A0A0J9X1Z3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X1Z3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.00 Å
  • R-Value Free:  0.463 (Depositor), 0.448 (DCC) 
  • R-Value Work:  0.441 (Depositor), 0.426 (DCC) 
  • R-Value Observed: 0.442 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 358.336α = 90
b = 358.336β = 90
c = 358.336γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description