9WE2 | pdb_00009we2

Crystal structure of HLA-A*11:01 bound to A0PXA8-V2 peptide(IVGAVGIAK)

• PDB DOI: https://doi.org/10.2210/pdb9WE2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Clostridium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-08-19 Released: 2026-08-26 
• Deposition Author(s): Jin, X.Y., Zhang, Z.Y., Xi, Y.H., Gu, Y.H., Qi, J.X., Chai, Y., Tan, S.G., Gao, G.F.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

Literature

Commensal Clostridium spp. harbor mimetic CTL-epitopes eliciting T cells cross-recognizing KRAS-G12V tumor neoantigen

Jin, X.Y., Wang, W.L., Zhang, Z.Y., Gu, Y.H., Xi, Y.H., Jiang, M., Peng, Y.Q., Yao, P.J., Tang, L.F., Ma, K.K., Wang, J., Li, F.Y., Li, X.W., Jin, W.J., Chen, Y., Chai, Y., Qi, J.X., Zhang, C.W.H., Liu, K.F., Wang, J., Gao, G.F., Tan, S.G.

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: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 89.39 kDa 
• Atom Count: 6,607 
• Modeled Residue Count: 764 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A, D	276	Homo sapiens	Mutation(s): 3  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A0PXA8-V2	C, F	9	Clostridium	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.753	α = 90
b = 67.127	β = 113.033
c = 91.695	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-26 
Deposition Author(s): Jin, X.Y., Zhang, Z.Y., Xi, Y.H., Gu, Y.H., Qi, J.X., Chai, Y., Tan, S.G., Gao, G.F.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2302900
Chinese Academy of Sciences	China	YSBR-083
National Natural Science Foundation of China (NSFC)	China	32222031

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release