1QHD

CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion.

Mathieu, M., Petitpas, I., Navaza, J., Lepault, J., Kohli, E., Pothier, P., Prasad, B.V., Cohen, J., Rey, F.A.

(2001) EMBO J. 20: 1485-1497

  • DOI: 10.1093/emboj/20.7.1485

  • PubMed Abstract: 

    • The structural protein VP6 of rotavirus, an important pathogen responsible for severe gastroenteritis in children, forms the middle layer in the triple-layered viral capsid. Here we present the crystal structure of VP6 determined to 2 A resolution an ...

    The structural protein VP6 of rotavirus, an important pathogen responsible for severe gastroenteritis in children, forms the middle layer in the triple-layered viral capsid. Here we present the crystal structure of VP6 determined to 2 A resolution and describe its interactions with other capsid proteins by fitting the atomic model into electron cryomicroscopic reconstructions of viral particles. VP6, which forms a tight trimer, has two distinct domains: a distal beta-barrel domain and a proximal alpha-helical domain, which interact with the outer and inner layer of the virion, respectively. The overall fold is similar to that of protein VP7 from bluetongue virus, with the subunits wrapping about a central 3-fold axis. A distinguishing feature of the VP6 trimer is a central Zn(2+) ion located on the 3-fold molecular axis. The crude atomic model of the middle layer derived from the fit shows that quasi-equivalence is only partially obeyed by VP6 in the T = 13 middle layer and suggests a model for the assembly of the 260 VP6 trimers onto the T = 1 viral inner layer.

    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Rotavirus Protein Vp6
      Petitpas, I.,Lepault, J.,Vachette, P.,Charpilienne, A.,Mathieu, M.,Kohli, E.,Pothier, P.,Cohen, J.,Rey, F.A.
      (1998) J.Virol. 72: 7615

    Organizational Affiliation: 

    Laboratoire de Génétique des Virus, CNRS-UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VIRAL CAPSID VP6
A
398Rotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1])Mutation(s): 0 
Find proteins for P04509 (Rotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1]))
Go to UniProtKB:  P04509
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.188 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 157.780α = 90.00
b = 157.780β = 90.00
c = 157.780γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance