9X85 | pdb_00009x85

Complex of HLA-DR4, a class II MHC, with a TGFbetaR2(-1) peptide

• PDB DOI: https://doi.org/10.2210/pdb9X85/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-18 Released: 2026-10-28 
• Deposition Author(s): Shi, J.L., Wu, D.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Models: experimental

Literature

Structural basis for CD4+ T cell receptor recognition of HLA-DR4-presented frameshift neoantigen derived from TGFbetaR2(-1).

Shi, J.L., Wu, D.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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: 45.01 kDa 
• Atom Count: 3,100 
• Modeled Residue Count: 377 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	181	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen DR beta chain	B	189	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt
Find proteins for A0A1V1IGJ9 (Homo sapiens) Explore A0A1V1IGJ9  Go to UniProtKB:  A0A1V1IGJ9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mutant human TGFbetaR2	C	16	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.34	α = 90
b = 103.32	β = 90
c = 114.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Shi, J.L., Wu, D.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270995

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release