Crystal structure of the p53 (Y107H) core domain orthorhombic P form

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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An African-Specific Variant of TP53 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression.

Indeglia, A.Leung, J.C.Miller, S.A.Leu, J.I.Dougherty, J.F.Clarke, N.L.Kirven, N.A.Shao, C.Ke, L.Lovell, S.Barnoud, T.Lu, D.Y.Lin, C.Kannan, T.Battaile, K.P.Yang, T.H.L.Batista Oliva, I.Claiborne, D.T.Vogel, P.Liu, L.Liu, Q.Nefedova, Y.Cassel, J.Auslander, N.Kossenkov, A.V.Karanicolas, J.Murphy, M.E.

(2023) Cancer Discov 13: 1696-1719

  • DOI: https://doi.org/10.1158/2159-8290.CD-22-1315
  • Primary Citation of Related Structures:  
    8E7A, 8E7B

  • PubMed Abstract: 

    TP53 is the most frequently mutated gene in cancer, yet key target genes for p53-mediated tumor suppression remain unidentified. Here, we characterize a rare, African-specific germline variant of TP53 in the DNA-binding domain Tyr107His (Y107H). Nuclear magnetic resonance and crystal structures reveal that Y107H is structurally similar to wild-type p53. Consistent with this, we find that Y107H can suppress tumor colony formation and is impaired for the transactivation of only a small subset of p53 target genes; this includes the epigenetic modifier PADI4, which deiminates arginine to the nonnatural amino acid citrulline. Surprisingly, we show that Y107H mice develop spontaneous cancers and metastases and that Y107H shows impaired tumor suppression in two other models. We show that PADI4 is itself tumor suppressive and that it requires an intact immune system for tumor suppression. We identify a p53-PADI4 gene signature that is predictive of survival and the efficacy of immune-checkpoint inhibitors.

  • Organizational Affiliation

    Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53220Homo sapiensMutation(s): 1 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.14α = 90
b = 109.484β = 90
c = 33.865γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description