8XY4 | pdb_00008xy4

Crystal structure of VACV N1 protein

PDB DOI: https://doi.org/10.2210/pdb8XY4/pdb

Classification: VIRAL PROTEIN
Organism(s): Orthopoxvirus vaccinia
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-19 Released: 2025-01-22
Deposition Author(s): Ni, X.C., Lei, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.170 (Depositor), 0.179 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into MPXV P1 protein and its orthologs reveal conformational dynamics and a conserved antiviral pocket.

Ni, X., Wang, Y., Fan, X., Yu, J., Lei, J.

(2025) Emerg Microbes Infect 14: 2515408-2515408

PubMed: 40476512 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1080/22221751.2025.2515408
Primary Citation Related Structures:
8XY1, 8XY2, 8XY3, 8XY4

Organizational Affiliation

National Clinical Research Center for Geriatrics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.

Macromolecule Content

Total Structure Weight: 16.15 kDa
Atom Count: 1,120
Modeled Residue Count: 122
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N1L	A	136	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: VACV_BRZ_SERRO2_026, N1L, 44/47.1_rMVA_020, List025, m8028L, mO028L
UniProt
Find proteins for P21054 (Vaccinia virus (strain Copenhagen)) Explore P21054 Go to UniProtKB: P21054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21054
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.170 (Depositor), 0.179 (DCC)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.86	α = 90
b = 77.86	β = 90
c = 111.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFF0702004

Revision History (Full details and data files)

Version 1.0: 2025-01-22
Type: Initial release
Version 1.1: 2025-07-02
Changes: Database references

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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.