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)

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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

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 
• DOI: https://doi.org/10.1080/22221751.2025.2515408
• Primary Citation of Related Structures:  
  8XY1, 8XY2, 8XY3, 8XY4

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, cross-linking

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

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

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Ni, X.C., Lei, J.

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

Revision History  

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