2OBR | pdb_00002obr

Crystal Structures of P Domain of Norovirus VA387

• PDB DOI: https://doi.org/10.2210/pdb2OBR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-20 Released: 2007-04-24 
• Deposition Author(s): Cao, S., Lou, Z., Jiang, X., Zhang, X.C., Li, X., Rao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.297 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the recognition of blood group trisaccharides by norovirus.

Cao, S., Lou, Z., Tan, M., Chen, Y., Liu, Y., Zhang, Z., Zhang, X.C., Jiang, X., Li, X., Rao, Z.

(2007) J Virol 81: 5949-5957

• PubMed: 17392366 
• DOI: https://doi.org/10.1128/JVI.00219-07
• Primary Citation Related Structures: 
  2OBR, 2OBS, 2OBT


• PubMed Abstract: 
  

  Noroviruses are one of the major causes of nonbacterial gastroenteritis epidemics in humans. Recent studies on norovirus receptors show that different noroviruses recognize different human histo-blood group antigens (HBGAs), and eight receptor binding patterns of noroviruses have been identified. The P domain of the norovirus capsids is directly involved in this recognition. To determine the precise locations and receptor binding modes of HBGA carbohydrates on the viral capsids, a recombinant P protein of a GII-4 strain norovirus, VA387, was cocrystallized with synthetic type A or B trisaccharides. Based on complex crystal structures observed at a 2.0-A resolution, we demonstrated that the receptor binding site lies at the outermost end of the P domain and forms an extensive hydrogen-bonding network with the saccharide ligand. The A and B trisaccharides display similar binding modes, and the common fucose ring plays a key role in this interaction. The extensive interface between the two protomers in a P dimer also plays a crucial role in the formation of the receptor binding interface.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.98 kDa 
• Atom Count: 2,535 
• Modeled Residue Count: 296 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	327	Norovirus	Mutation(s): 2
UniProt
Find proteins for Q913Z3 (Human calicivirus NLV/VA98387/1998) Explore Q913Z3  Go to UniProtKB:  Q913Z3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.297 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.333	α = 90
b = 97.439	β = 90
c = 118.912	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Cao, S., Lou, Z., Jiang, X., Zhang, X.C., Li, X., Rao, Z.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description