8J5B

Crystal structure of P domain from norovirus GI.4 capsid protein.

• PDB DOI: https://doi.org/10.2210/pdb8J5B/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-21 Released: 2024-04-24 
• Deposition Author(s): Katsura, K., Sakai, N., Hasegawa, K., Kimura-Someya, T., Shirouzu, M.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.275 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Crystal structure of P domain from norovirus GI.4 capsid protein.

Katsura, K.

To be published.

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 Evidence: gel filtration

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: 132.56 kDa 
• Atom Count: 9,579 
• Modelled Residue Count: 1,198 
• Deposited Residue Count: 1,228 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	314	Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden	Mutation(s): 0  Gene Names: ORF2
UniProt
Find proteins for H2DG73 (Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden) Explore H2DG73  Go to UniProtKB:  H2DG73

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	B, C	303	Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden	Mutation(s): 0  Gene Names: ORF2
UniProt
Find proteins for H2DG73 (Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden) Explore H2DG73  Go to UniProtKB:  H2DG73

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	D	308	Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden	Mutation(s): 0  Gene Names: ORF2
UniProt
Find proteins for H2DG73 (Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden) Explore H2DG73  Go to UniProtKB:  H2DG73

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.275 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.673	α = 91.74
b = 62.791	β = 97.71
c = 92.756	γ = 119.07

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Katsura, K., Sakai, N., Hasegawa, K., Kimura-Someya, T., Shirouzu, M.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release