6RZ3

Crystal structure of a complex between the DNA-binding domain of p53 and the carboxyl-terminal conserved region of iASPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.23 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

iASPP mediates p53 selectivity through a modular mechanism fine-tuning DNA recognition.

Chen, S.Wu, J.Zhong, S.Li, Y.Zhang, P.Ma, J.Ren, J.Tan, Y.Wang, Y.Au, K.F.Siebold, C.Bond, G.L.Chen, Z.Lu, M.Jones, E.Y.Lu, X.

(2019) Proc Natl Acad Sci U S A 116: 17470-17479

  • DOI: https://doi.org/10.1073/pnas.1909393116
  • Primary Citation of Related Structures:  
    6RZ3

  • PubMed Abstract: 

    The most frequently mutated protein in human cancer is p53, a transcription factor (TF) that regulates myriad genes instrumental in diverse cellular outcomes including growth arrest and cell death. Cell context-dependent p53 modulation is critical for this life-or-death balance, yet remains incompletely understood. Here we identify sequence signatures enriched in genomic p53-binding sites modulated by the transcription cofactor iASPP. Moreover, our p53-iASPP crystal structure reveals that iASPP displaces the p53 L1 loop-which mediates sequence-specific interactions with the signature-corresponding base-without perturbing other DNA-recognizing modules of the p53 DNA-binding domain. A TF commonly uses multiple structural modules to recognize its cognate DNA, and thus this mechanism of a cofactor fine-tuning TF-DNA interactions through targeting a particular module is likely widespread. Previously, all tumor suppressors and oncoproteins that associate with the p53 DNA-binding domain-except the oncogenic E6 from human papillomaviruses (HPVs)-structurally cluster at the DNA-binding site of p53, complicating drug design. By contrast, iASPP inhibits p53 through a distinct surface overlapping the E6 footprint, opening prospects for p53-targeting precision medicine to improve cancer therapy.


  • Organizational Affiliation

    Department of Internal Medicine, University of Iowa, Iowa City, IA 52242.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53232Homo sapiensMutation(s): 0 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RelA-associated inhibitor238Homo sapiensMutation(s): 0 
Gene Names: PPP1R13LIASPPNKIP1PPP1R13BLRAI
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUF5 (Homo sapiens)
Explore Q8WUF5 
Go to UniProtKB:  Q8WUF5
GTEx:  ENSG00000104881 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUF5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.23 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.247 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.09α = 90
b = 71.09β = 90
c = 255.589γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description