5E6T | pdb_00005e6t

Crystal structure of bovine norovirus P domain

• PDB DOI: https://doi.org/10.2210/pdb5E6T/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus Bo/GIII/B309/2003/BEL
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-10 Released: 2015-12-09 
• Deposition Author(s): Singh, B.K., Hansman, G.S.
• Funding Organization(s): CHS foundation, Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of bovine norovirus protruding domain.

Singh, B.K., Koromyslova, A., Hansman, G.S.

(2015) Virology 487: 296-301

• PubMed: 26599362 
• DOI: https://doi.org/10.1016/j.virol.2015.10.022
• Primary Citation Related Structures: 
  5E6T


• PubMed Abstract: 
  

  We determined a structure of a bovine (genogroup III, GIII) norovirus capsid protruding (P) domain using X-ray crystallography. The bovine P domain was reminiscent of other norovirus genogroups (GI, GII, GIV, and GV), but closely matched the human GI P domain. We also identified a monoclonal antibody that was capable of binding the five different (GI-GV) P domains. Our data suggests that genetically diverse noroviruses still contain common epitopes.

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Organizational Affiliation: 
• Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany.
Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 63.24 kDa 
• Atom Count: 4,614 
• Modeled Residue Count: 572 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid	A, B	288	Norovirus Bo/GIII/B309/2003/BEL	Mutation(s): 0
UniProt
Find proteins for E6Y5B1 (Norovirus Bo/GIII/B309/2003/BEL) Explore E6Y5B1  Go to UniProtKB:  E6Y5B1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.92	α = 90
b = 63.86	β = 115.06
c = 87.56	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Singh, B.K., Hansman, G.S.

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Funding Organization	Location	Grant Number
CHS foundation	Germany	--
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description