9OLU | pdb_00009olu

GX/NPIH26 bat norovirus protruding domain in complex with L-fucose

PDB DOI: https://doi.org/10.2210/pdb9OLU/pdb

Classification: VIRAL PROTEIN
Organism(s): Bat norovirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-13 Released: 2025-07-16
Deposition Author(s): Holroyd, D.L., Bruning, J.B., Hansman, G.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.194 (Depositor), 0.192 (DCC)
R-Value Work:
0.158 (Depositor), 0.157 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural constraints prevent a bat norovirus from binding to histo-blood group antigen co-factors.

Holroyd, D.L., Bruning, J.B., von Itzstein, M., Hansman, G.S.

(2025) J Virol 99: e0099525-e0099525

PubMed: 40879379 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.00995-25
Primary Citation Related Structures:
9OLT, 9OLU

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 64.9 kDa
Atom Count: 5,540
Modeled Residue Count: 594
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S1TZT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC (Subject of Investigation/LOI) Query on FUC Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.194 (Depositor), 0.192 (DCC)
R-Value Work: 0.158 (Depositor), 0.157 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.542	α = 90
b = 67.542	β = 90
c = 238.385	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release
Version 1.1: 2026-01-21
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.