1WQS | pdb_00001wqs

Crystal structure of Norovirus 3C-like protease

PDB DOI: https://doi.org/10.2210/pdb1WQS/pdb

Classification: HYDROLASE
Organism(s): Chiba virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-10-01 Released: 2005-10-04
Deposition Author(s): Nakamura, K., Someya, Y., Kumasaka, T., Tanaka, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.240 (Depositor), 0.205 (DCC)
R-Value Work:
0.206 (Depositor), 0.209 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A norovirus protease structure provides insights into active and substrate binding site integrity

Nakamura, K., Someya, Y., Kumasaka, T., Ueno, G., Yamamoto, M., Sato, T., Takeda, N., Miyamura, T., Tanaka, N.

(2005) J Virol 79: 13685-13693

PubMed: 16227288 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JVI.79.21.13685-13693.2005
Primary Citation Related Structures:
1WQS

PubMed Abstract:
Norovirus 3C-like proteases are crucial to proteolytic processing of norovirus polyproteins. We determined the crystal structure of the 3C-like protease from Chiba virus, a norovirus, at 2.8-A resolution. An active site including Cys139 and His30 is present, as is a hydrogen bond network that stabilizes the active site conformation. In the oxyanion hole backbone, a structural difference was observed probably upon substrate binding. A peptide substrate/enzyme model shows that several interactions between the two components are critical for substrate binding and that the S1 and S2 sites appropriately accommodate the substrate P1 and P2 residues, respectively. Knowledge of the structure and a previous mutagenesis study allow us to correlate proteolysis and structure.

Organizational Affiliation

Department of Life Science, Tokyo Institute of Technology, Yokohama 226-8501, Japan.

Macromolecule Content

Total Structure Weight: 76.23 kDa
Atom Count: 5,367
Modeled Residue Count: 692
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like protease	A, B, C, D	173	Chiba virus	Mutation(s): 0
UniProt
Find proteins for Q9DU47 (Chiba virus (strain GI/Human/Japan/Chiba 407/1987)) Explore Q9DU47 Go to UniProtKB: Q9DU47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9DU47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth C] E [auth A], F [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D]
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.240 (Depositor), 0.205 (DCC)
R-Value Work: 0.206 (Depositor), 0.209 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.89	α = 90
b = 128.89	β = 90
c = 118.08	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-10-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-04
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-12-25
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary