8J5B | pdb_00008j5b

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.275 (Depositor), 0.278 (DCC)
R-Value Work:
0.232 (Depositor), 0.236 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

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

Katsura, K.

To be published.

Macromolecule Content

Total Structure Weight: 132.56 kDa
Atom Count: 9,579
Modeled Residue Count: 1,198
Deposited Residue Count: 1,228
Unique protein chains: 3

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H2DG73
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H2DG73
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H2DG73
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.275 (Depositor), 0.278 (DCC)
R-Value Work: 0.232 (Depositor), 0.236 (DCC)
R-Value Observed: 0.234 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

Kimura-Someya, T.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.