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 9X7R | pdb_00009x7r

The molecular mechanisms of CD8+ T cell responses to restrictive UTP20 antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free: 
    0.279 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9X7R

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: 93.52 kDa 
  • Atom Count: 6,543 
  • Modeled Residue Count: 815 
  • Deposited Residue Count: 818 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR alphaA [auth D]189Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR betaB [auth E]244Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigenC [auth A]276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for Q8WLS4 (Homo sapiens)
Explore Q8WLS4 
Go to UniProtKB:  Q8WLS4
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UniProt GroupQ8WLS4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth B]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 
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UniProt GroupP61769
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
peptideE [auth C]9Homo sapiensMutation(s): 0 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free:  0.279 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.02α = 90
b = 204.02β = 90
c = 204.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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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