Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 45.21 kDa 
• Atom Count: 3473 
• Residue Count: 398 
• Unique protein chains: 1

1QHD

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

• DOI: 10.2210/pdb1QHD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bovine rotavirus strain RF
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1999-04-29 Released: 2001-04-13 
• Deposition Author(s): Mathieu, M., Petitpas, I., Rey, F.A.

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Experimental Data Snapshot

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

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

• PubMed: 11285213 
• DOI: 10.1093/emboj/20.7.1485
• Primary Citation of Related Structures:  
  1QHD


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VIRAL CAPSID VP6	A	398	Bovine rotavirus strain RF	Mutation(s): 0  Gene Names: SEGMENT 6
Find proteins for P04509 (Rotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1])) Explore P04509  Go to UniProtKB:  P04509

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 157.78	α = 90
b = 157.78	β = 90
c = 157.78	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-29 
• Released Date: 2001-04-13 
Deposition Author(s): Mathieu, M., Petitpas, I., Rey, F.A.

Revision History 

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