9OLT | pdb_00009olt

GII.27: Loreto0959 norovirus protruding domain complexed with A-trisaccharide

PDB DOI: https://doi.org/10.2210/pdb9OLT/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus GII
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-13 Released: 2025-07-09
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: 1.76 Å
R-Value Free:
0.196 (Depositor), 0.194 (DCC)
R-Value Work:
0.149 (Depositor), 0.147 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/jvi.00995-25
Primary Citation of 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: 69.61 kDa
Atom Count: 5,680
Modeled Residue Count: 619
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	310	Norovirus GII	Mutation(s): 0
UniProt
Find proteins for A0A2H4Y8Z8 (Norovirus GII) Explore A0A2H4Y8Z8 Go to UniProtKB: A0A2H4Y8Z8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2H4Y8Z8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	C	3		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G15611BA GlyCosmos: G15611BA GlyGen: G15611BA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]