9EDQ | pdb_00009edq

GX/NPIH26 bat norovirus protruding domain

• PDB DOI: https://doi.org/10.2210/pdb9EDQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bat norovirus
• Expression System: Escherichia coli
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

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

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Organizational Affiliation: 
• Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
Institute for Biomedicine and Glycomics (IBG), Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia.

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: 64.96 kDa 
• Atom Count: 5,682 
• Modeled Residue Count: 594 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	297	Bat norovirus	Mutation(s): 0  Gene Names: ORF2
UniProt
Find proteins for A0A2S1TZT6 (Bat norovirus) Explore A0A2S1TZT6  Go to UniProtKB:  A0A2S1TZT6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.49	α = 90
b = 67.49	β = 90
c = 238.76	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Holroyd, D.L., Kumar, A., Bruning, J.B., Hansman, G.S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• 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