6RZ3 | pdb_00006rz3

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 (Depositor), 0.313 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6RZ3

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 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
    • Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 51.86 kDa 
  • Atom Count: 2,867 
  • Modeled Residue Count: 368 
  • Deposited Residue Count: 470 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  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
PHAROS:  Q8WUF5
GTEx:  ENSG00000104881 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUF5
Sequence Annotations
Expand
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 (Depositor), 0.313 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
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