8JV0

Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution

• PDB DOI: https://doi.org/10.2210/pdb8JV0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Sus scrofa, Asfivirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-27 Released: 2024-06-05 
• Deposition Author(s): Wang, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution

Wang, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 88.56 kDa 
• Atom Count: 6,333 
• Modelled Residue Count: 763 
• Deposited Residue Count: 764 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	275	Sus scrofa	Mutation(s): 0  Gene Names: SLA-2
UniProt
Find proteins for B1A9P1 (Sus scrofa) Explore B1A9P1  Go to UniProtKB:  B1A9P1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	98	Sus scrofa	Mutation(s): 0  Gene Names: B2M
UniProt
Find proteins for Q07717 (Sus scrofa) Explore Q07717  Go to UniProtKB:  Q07717

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR	C, F	9	Asfivirus	Mutation(s): 0
UniProt
Find proteins for P0C9J3 (African swine fever virus (isolate Warthog/Namibia/Wart80/1980)) Explore P0C9J3  Go to UniProtKB:  P0C9J3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.944	α = 90
b = 105.317	β = 90
c = 221.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Wang, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary