8JRK

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Crystal structure of the bat MHC II molecule at 2.3 A 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 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

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

Macromolecules

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

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

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 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• 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

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: 2024-10-09
  Changes: Structure summary