9HY4 | pdb_00009hy4

Solubly expressed miniaturized SMART H2-Db

• PDB DOI: https://doi.org/10.2210/pdb9HY4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Mammarenavirus choriomeningitidis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-09 Released: 2025-12-31 
• Deposition Author(s): Sun, R., White, W., Bai, H., Baker, D., Achour, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.281 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: in silico

Literature

Design of solubly expressed miniaturized SMART MHCs

White, W., Baker, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.22 kDa 
• Atom Count: 4,076 
• Modeled Residue Count: 480 
• Deposited Residue Count: 528 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A, C	255	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus) Explore P01899  Go to UniProtKB:  P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET	B, D	9	Mammarenavirus choriomeningitidis	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.281 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.954	α = 90
b = 93.237	β = 94.08
c = 75.856	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Sun, R., White, W., Bai, H., Baker, D., Achour, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release