8Z0H | pdb_00008z0h

Crystal structure of 9-mer peptide from ALV-J in complex with BF2*0201

PDB DOI: https://doi.org/10.2210/pdb8Z0H/pdb

Classification: IMMUNE SYSTEM
Organism(s): Gallus gallus, Avian leukemia virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-09 Released: 2025-01-15
Deposition Author(s): Jia, Y.S., Ma, M.L., Li, Y.L., Liao, M., Dai, M.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.212 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.192 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Z0H

This is version 1.1 of the entry. See complete history.

Literature

Structure and Mechanism of ALV-J Epitope Presented by MHC Class I Molecule BF20201

Jia, Y.S., Li, Y.L., Ma, M.L., Liao, M., Dai, M.M.

(2024) Xu Mu Shou Yi Xue Bao 55: 3132-3142

DOI: https://doi.org/10.11843/j.issn.0366-6964.2024.07.031

Macromolecule Content

Total Structure Weight: 172.64 kDa
Atom Count: 13,619
Modeled Residue Count: 1,516
Deposited Residue Count: 1,516
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I alpha chain 2	A, C [auth D], E [auth G], G [auth J]	273	Gallus gallus	Mutation(s): 0 Gene Names: B-FIV, BF2
UniProt
Find proteins for O46789 (Gallus gallus) Explore O46789 Go to UniProtKB: O46789
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O46789
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D [auth E], F [auth H], H [auth K]	97	Gallus gallus	Mutation(s): 0 Gene Names: B2M
UniProt
Find proteins for P21611 (Gallus gallus) Explore P21611 Go to UniProtKB: P21611
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21611
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag protein	I, J [auth C], K [auth F], L	9	Avian leukemia virus	Mutation(s): 0
UniProt
Find proteins for G0Z7Q1 (Avian leukosis virus) Explore G0Z7Q1 Go to UniProtKB: G0Z7Q1
Entity Groups
UniProt Group	G0Z7Q1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.212 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.192 (DCC)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.614	α = 90
b = 115.584	β = 111.158
c = 94.107	γ = 90

Software Package:

Software Name	Purpose
DIALS	data reduction
DIALS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release
Version 1.1: 2025-02-05
Changes: Database references

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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.