9R34 | pdb_00009r34

Norovirus NS3 hexamer in complex with ATP-gamma-S

PDB DOI: https://doi.org/10.2210/pdb9R34/pdb
EM Map EMD-53547: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Norwalk virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-02 Released: 2025-10-29
Deposition Author(s): Haas, M., Hurdiss, D.L.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9R34

This is version 1.0 of the entry. See complete history.

Literature

Integrative Structure of Norovirus NS3 Suggests a Role in RNA Transport

Haas, M., Mills, J.T., Kelley, C., Das, A., Hof, H., Niemel, C., Donselaar, T., Drulyte, I., van Kuppeveld, F.J., Dulin, D., Snijder, J., Herod, M.R., Hurdiss, D.L.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.06.17.659504

Macromolecule Content

Total Structure Weight: 232.9 kDa
Atom Count: 14,232
Modeled Residue Count: 1,800
Deposited Residue Count: 2,136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTPase	A, B, C, D, E A, B, C, D, E, F	356	Norwalk virus	Mutation(s): 0 Gene Names: ORF1 EC: 3.6.1.15
UniProt
Find proteins for Q83883 (Norovirus (strain Human/NoV/United States/Norwalk/1968/GI)) Explore Q83883 Go to UniProtKB: Q83883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain M [auth D] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	VI.Veni.212.102
European Research Council (ERC)	European Union	101164550

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

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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.