9EDP | pdb_00009edp

GVIII-Chiba040502 norovirus protruding domain

PDB DOI: https://doi.org/10.2210/pdb9EDP/pdb

Classification: VIRAL PROTEIN
Organism(s): Chiba-040502 virus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-11-17 Released: 2025-03-05
Deposition Author(s): Holroyd, D.L., Kumar, A., Bruning, J.B., Hansman, G.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.140 (Depositor), 0.139 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Antigenic structural analysis of bat and human norovirus protruding (P) domains.

Holroyd, D.L., Kumar, A., Vasquez, E., Masic, V., von Itzstein, M., Bruning, J.B., Hansman, G.S.

(2025) J Virol 99: e0197124-e0197124

PubMed: 40062838 Search on PubMed
DOI: https://doi.org/10.1128/jvi.01971-24
Primary Citation Related Structures:
9EDM, 9EDN, 9EDO, 9EDP, 9EDQ

Organizational Affiliation

Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.

Macromolecule Content

Total Structure Weight: 35.67 kDa
Atom Count: 3,250
Modeled Residue Count: 305
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	320	Chiba-040502 virus	Mutation(s): 0
UniProt
Find proteins for Q3V574 (Chiba-040502 virus) Explore Q3V574 Go to UniProtKB: Q3V574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3V574
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.140 (Depositor), 0.139 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.241	α = 90
b = 107.241	β = 90
c = 61.577	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-03-05
Type: Initial release
Version 1.1: 2025-03-19
Changes: Database references
Version 1.2: 2025-04-23
Changes: Database references

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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.