8W6L | pdb_00008w6l

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

PDB DOI: https://doi.org/10.2210/pdb8W6L/pdb

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

Deposited: 2023-08-29 Released: 2024-08-07
Deposition Author(s): Wang, S.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.277 (Depositor), 0.293 (DCC)
R-Value Work:
0.238 (Depositor), 0.246 (DCC)
R-Value Observed:
0.240 (Depositor)

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

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

Wang, S.

To be published.

Macromolecule Content

Total Structure Weight: 44.29 kDa
Atom Count: 3,159
Modeled Residue Count: 379
Deposited Residue Count: 382
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	275	Sus scrofa	Mutation(s): 0 Gene Names: SLA-2
UniProt
Find proteins for B1A9P1 (Sus scrofa) Explore B1A9P1 Go to UniProtKB: B1A9P1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1A9P1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	98	Sus scrofa	Mutation(s): 0 Gene Names: B2M
UniProt
Find proteins for Q07717 (Sus scrofa) Explore Q07717 Go to UniProtKB: Q07717
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07717
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-MET-TYR-SER-LEU-GLY-TYR-ILE-PHE	C	9	Asfivirus	Mutation(s): 0
UniProt
Find proteins for Q89702 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore Q89702 Go to UniProtKB: Q89702
Entity Groups
UniProt Group	Q89702
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.277 (Depositor), 0.293 (DCC)
R-Value Work: 0.238 (Depositor), 0.246 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.531	α = 94.4
b = 48.883	β = 101.86
c = 51.173	γ = 100.92

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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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.