8XY3 | pdb_00008xy3

Crystal structure of VARV P1 protein

• PDB DOI: https://doi.org/10.2210/pdb8XY3/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Variola virus
• 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: 2.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.41 kDa 
• Atom Count: 4,157 
• Modeled Residue Count: 472 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P1L	A [auth C], B, C [auth D], D [auth A]	136	Variola virus	Mutation(s): 0  Gene Names: R1L
UniProt
Find proteins for P34018 (Variola virus (isolate Human/India/Ind3/1967)) Explore P34018  Go to UniProtKB:  P34018

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.064	α = 90
b = 153.786	β = 90
c = 132.146	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	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