4P25

Structure of the P domain from a GI.7 Norovirus variant in complex with LeY HBGA.

• PDB DOI: https://doi.org/10.2210/pdb4P25/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus Hu/GI.7/TCH-060/USA/2003
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-01 Released: 2014-04-02 
• Deposition Author(s): Shanker, S., Czako, R., Sankaran, B., Atmar, R., Estes, M., Prasad, B.V.V.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.174 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 133.46 kDa 
• Atom Count: 10,155 
• Modelled Residue Count: 1,153 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D	302	Norovirus Hu/GI.7/TCH-060/USA/2003	Mutation(s): 0
UniProt
Find proteins for G8FL04 (Norovirus Hu/GI.7/TCH-060/USA/2003) Explore G8FL04  Go to UniProtKB:  G8FL04

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	4		N/A
Glycosylation Resources
GlyTouCan:  G00052MO GlyCosmos:  G00052MO GlyGen:  G00052MO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900054	E, F, G, H	Lewis Y antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.174 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.314	α = 72.8
b = 63.124	β = 82.18
c = 90.58	γ = 60.85

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Shanker, S., Czako, R., Sankaran, B., Atmar, R., Estes, M., Prasad, B.V.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 2.0: 2019-11-27
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 3.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary