5YSX

Structure of P domain of GII.2 Noroviruses

• PDB DOI: https://doi.org/10.2210/pdb5YSX/pdb

• Classification: CELL ADHESION
• Organism(s): Norovirus GII
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-08-08 
• Deposition Author(s): Duan, Z., Ao, Y.
• Funding Organization(s): Special National Project on Research and Development of Key Biosafety Technologies

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.167 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Genetic Analysis of Reemerging GII.P16-GII.2 Noroviruses in 2016-2017 in China.

Ao, Y., Cong, X., Jin, M., Sun, X., Wei, X., Wang, J., Zhang, Q., Song, J., Yu, J., Cui, J., Qi, J., Tan, M., Duan, Z.

(2018) J Infect Dis 218: 133-143

• PubMed: 29617875 
• DOI: https://doi.org/10.1093/infdis/jiy182
• Primary Citation of Related Structures:  
  5YSX


• PubMed Abstract: 
  

  During 2016-2017, the previously rare GII.P16-GII.2 norovirus suddenly emerged as the predominant genotype causing gastroenteritis outbreaks in China and other countries. Its origin, phylodynamics, and mechanism behind the predominance remain unclear.

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Organizational Affiliation: 

National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,851 
• Modelled Residue Count: 309 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	309	Norovirus GII	Mutation(s): 0
UniProt
Find proteins for A0A2R3BZ02 (Norovirus GII) Explore A0A2R3BZ02  Go to UniProtKB:  A0A2R3BZ02

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.167 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.534	α = 90
b = 96.534	β = 90
c = 64.319	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Duan, Z., Ao, Y.

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Funding Organization	Location	Grant Number
Special National Project on Research and Development of Key Biosafety Technologies	China	Grant No. 2016YFC1201900

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description