3ASS

Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with Lewis-b

• PDB DOI: https://doi.org/10.2210/pdb3ASS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norwalk-like virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-17 Released: 2012-01-25 
• Deposition Author(s): Kubota, T., Kumagai, A., Itoh, H., Furukawa, S., Narimatsu, H., Wakita, T., Ishii, K., Takeda, N., Someya, Y., Shirato, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

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: 72.19 kDa 
• Atom Count: 5,218 
• Modelled Residue Count: 613 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	326	Norwalk-like virus	Mutation(s): 0  Gene Names: capsid, ORF2
UniProt
Find proteins for Q8JW44 (Norwalk-like virus) Explore Q8JW44  Go to UniProtKB:  Q8JW44

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G00048MO GlyCosmos:  G00048MO GlyGen:  G00048MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPO	F [auth A], G [auth B]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
NA	E [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900123	C, D	Lewis B antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.69	α = 90
b = 74.69	β = 90
c = 106.973	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	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: 2012-01-25 
Deposition Author(s): Kubota, T., Kumagai, A., Itoh, H., Furukawa, S., Narimatsu, H., Wakita, T., Ishii, K., Takeda, N., Someya, Y., Shirato, H.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Database references
• 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