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), 0.290 (DCC)
R-Value Work:
0.238 (Depositor), 0.250 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1A9P1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.290 (DCC)
R-Value Work: 0.238 (Depositor), 0.250 (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

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.