8JRK | pdb_00008jrk

Crystal structure of the bat MHC II molecule at 2.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb8JRK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Eptesicus fuscus, Human coronavirus 229E
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-17 Released: 2024-06-05
Deposition Author(s): Wang, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.234 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.209 (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 bat MHC II molecule at 2.3 A resolution

Wang, S.

To be published.

Macromolecule Content

Total Structure Weight: 89.35 kDa
Atom Count: 6,234
Modeled Residue Count: 734
Deposited Residue Count: 770
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, D [auth C]	182	Eptesicus fuscus	Mutation(s): 0
UniProt
Find proteins for A0AAT8XUA5 (Eptesicus fuscus) Explore A0AAT8XUA5 Go to UniProtKB: A0AAT8XUA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAT8XUA5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II histocompatibility antigen, DR-1 beta chain	B, E [auth D]	190	Eptesicus fuscus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ASN-ASP-ILE-LEU-SER-ARG-LEU-ASP-PRO-PRO-GLU-ALA-SER	C [auth E], F	13	Human coronavirus 229E	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.234 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.946	α = 90
b = 91.946	β = 90
c = 214.109	γ = 90

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: 2024-06-05

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: 2024-06-05
Type: Initial release
Version 1.1: 2024-10-09
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.