9EDN | pdb_00009edn

GII.23: Loreto1847 norovirus protruding domain

PDB DOI: https://doi.org/10.2210/pdb9EDN/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus GII
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: 1.22 Å
R-Value Free:
0.146 (Depositor), 0.146 (DCC)
R-Value Work:
0.123 (Depositor), 0.123 (DCC)
R-Value Observed:
0.124 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 70.01 kDa
Atom Count: 6,547
Modeled Residue Count: 619
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

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| 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 A0A0U2T5K7 (Norovirus GII) Explore A0A0U2T5K7 Go to UniProtKB: A0A0U2T5K7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U2T5K7
Sequence Annotations Expand
Reference Sequence

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 C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B]	M [auth A], N [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B]