8PN6 | pdb_00008pn6

Crystal Structure of co-expressed NS2B-NS3 Protease from Zika Virus

PDB DOI: https://doi.org/10.2210/pdb8PN6/pdb

Classification: VIRAL PROTEIN
Organism(s): Zika virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-29 Released: 2023-08-16
Deposition Author(s): Ni, X., Fairhead, M., Balcomb, B.H., Aschenbrenner, J.C., Ferreira, L.M., Godoy, A.S., Lithgo, R.M., MacLean, E.M., Marples, P.G., Thompson, W., Tomlinson, C.W.E., Szommer, T., Wild, C., Wright, N.D., Koekemoer, L., Fearon, D., Walsh, M.A., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.258 (Depositor), 0.270 (DCC)
R-Value Work:
0.208 (Depositor), 0.220 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of co-expressed NS2B-NS3 Protease from Zika Virus

Ni, X., Fairhead, M., Balcomb, B.H., Aschenbrenner, J.C., Ferreira, L.M., Godoy, A.S., Lithgo, R.M., MacLean, E.M., Marples, P.G., Thompson, W., Tomlinson, C.W.E., Szommer, T., Wild, C., Wright, N.D., Koekemoer, L., Fearon, D., Walsh, M.A., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 23.19 kDa
Atom Count: 1,594
Modeled Residue Count: 195
Deposited Residue Count: 214
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	46	Zika virus	Mutation(s): 0
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B	168	Zika virus	Mutation(s): 0 Gene Names: GP1, A2G93_63394gpGP1
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.258 (Depositor), 0.270 (DCC)
R-Value Work: 0.208 (Depositor), 0.220 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.01	α = 90
b = 43.01	β = 90
c = 216.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Aschenbrenner, J.C.

Tomlinson, C.W.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171399

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2024-08-14
Changes: Author supporting evidence

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.