9LLU | pdb_00009llu

p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 
    0.270 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history

Literature

Structural basis for T-cell receptor recognition of p53 Y220D , a human cancer neoantigen.

Duan, Z.Zhao, J.Wu, J.Zhang, Y.Yuan, P.Zeng, Y.Jin, H.Mariuzza, R.A.Wu, D.

(2026) Acta Crystallogr D Struct Biol 

  • DOI: https://doi.org/10.1107/S2059798326007564
  • Primary Citation Related Structures: 
    21EX, 21GJ, 9LLU

  • PubMed Abstract: 

    Adoptive cell therapy (ACT) with tumor-specific T cells can mediate durable cancer regression. The main target of tumor-specific T cells are neoantigens resulting from mutations in self-antigens over the course of malignant transformation. To understand T-cell recognition of cancer neoantigens at the atomic level, we studied a T-cell receptor (TCR 4414A) that recognizes a neoepitope arising from a driver mutation in the p53 oncogene (p53 Y220D ) presented by HLA-A2. Here, we report the structure of TCR 4414A bound to HLA-A2 and p53 Y220D , as well as structures of unbound wild-type and mutant p53-HLA-A2 ligands. The structures reveal that the Y220D mutation induces a conformational change in the p53 Y220D neoepitope that is detected by TCR 4414A, thereby rendering a normally cryptic self-peptide visible to T cells. The TCR minimizes interactions with the N- and C-terminal portions of p53 Y220D , which are identical in mutant and wild-type peptides, and instead focuses on the Y220D driver mutation at the peptide center. In this way, TCR 4414A achieves highly specific recognition of mutant over wild-type p53, a critical parameter for avoiding off-target toxicities in ACT.


  • Organizational Affiliation
    • Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 95.83 kDa 
  • Atom Count: 6,610 
  • Modeled Residue Count: 820 
  • Deposited Residue Count: 839 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigen276Homo 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: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VAL-VAL-PRO-ASP-GLU-PRO-PRO-GLU-VAL9Homo sapiensMutation(s): 0 
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor 4414A chain betaD [auth E]247Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor 4414A chain alphaE [auth D]207Homo sapiensMutation(s): 0 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free:  0.270 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.64α = 90
b = 44.05β = 104.59
c = 207.879γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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
National Natural Science Foundation of China (NSFC)China32100982

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Database references