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 9XME | pdb_00009xme

Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9XME

This is version 1.0 of the entry. See complete history. 

Literature

Structural basis for CD8 + T cell recognition of the charge-reversed neoantigen UTP20 D2661H.

Wang, J., Li, S., Mao, L., Yang, D., Yao, Z., Shi, J., He, W., Wu, D.

(2026) J Struct Biol : 108371-108371

  • DOI: https://doi.org/10.1016/j.jsb.2026.108371
  • Primary Citation Related Structures: 
    9X7R, 9X7U, 9XME

  • PubMed Abstract: 

    Adoptive T cell therapy (ACT) eliminates tumors by infusing tumor reactive T cells. Neoantigens from somatic mutations are ideal targets due to their absence in normal tissues. How charge-reversing mutations drive neoantigen immunogenicity remains unclear. Here, we determined the wild-type and mutant UTP20-HLA-A2 structures and found them nearly identical except at the mutation site (Asp to His). The TCR-pHLA structure revealed selective recognition through specific interactions between CDR loops and the mutation site. Rosetta calculations showed that His provides favorable interactions absent in the wild-type. TCR engagement also induced a flip of the P6 side chain, reshaping the interface. These findings provide a structural basis for charge-reversed mutation-driven T cell responses and inform neoantigen-based ACT development.


  • Organizational Affiliation: 
    • Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.

Macromolecule Content 

  • Total Structure Weight: 89.65 kDa 
  • Atom Count: 7,031 
  • Modeled Residue Count: 766 
  • Deposited Residue Count: 770 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigen
A, D
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for Q8WLS4 (Homo sapiens)
Explore Q8WLS4 
Go to UniProtKB:  Q8WLS4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WLS4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
100Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small subunit processome component 20 homolog
C, F
9Homo sapiensMutation(s): 0 
Gene Names: UTP20, DRIM
UniProt & NIH Common Fund Data Resources
Find proteins for O75691 (Homo sapiens)
Explore O75691 
Go to UniProtKB:  O75691
PHAROS:  O75691
GTEx:  ENSG00000120800 
Entity Groups
UniProt GroupO75691
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.313α = 90
b = 83.912β = 90.12
c = 83.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
xia2data scaling
xia2data reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32270995

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-23
    Type: Initial release