3PVD

Crystal structure of P domain dimer of Norovirus VA207 complexed with 3'-sialyl-Lewis x tetrasaccharide

• PDB DOI: https://doi.org/10.2210/pdb3PVD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human calicivirus NLV/VA97207/1997
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-12-06 Released: 2011-08-03 
• Deposition Author(s): Chen, Y., Tan, M., Xia, M., Hao, N., Zhang, X.C., Huang, P., Jiang, X., Li, X., Rao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

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: 70.99 kDa 
• Atom Count: 5,121 
• Modelled Residue Count: 601 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid	A, B	316	Human calicivirus NLV/VA97207/1997	Mutation(s): 5  Gene Names: CAPSID
UniProt
Find proteins for Q91H09 (Human calicivirus NLV/VA97207/1997) Explore Q91H09  Go to UniProtKB:  Q91H09

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G07675NG GlyCosmos:  G07675NG GlyGen:  G07675NG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900122	C, D	Sialyl-Lewis X antigen, alpha anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.301	α = 90
b = 96	β = 90
c = 101.631	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Chen, Y., Tan, M., Xia, M., Hao, N., Zhang, X.C., Huang, P., Jiang, X., Li, X., Rao, Z.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary