2GEQ

Crystal Structure of a p53 Core Dimer Bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the p53 Core Domain Dimer Bound to DNA.

Ho, W.C.Fitzgerald, M.X.Marmorstein, R.

(2006) J Biol Chem 281: 20494-20502

  • DOI: 10.1074/jbc.M603634200
  • Primary Citation of Related Structures:  
    2GEQ

  • PubMed Abstract: 
  • The p53 tumor suppressor protein binds to DNA as a dimer of dimers to regulate transcription of genes that mediate responses to cellular stress. We have prepared a cross-linked trapped p53 core domain dimer bound to decamer DNA and have determined its structure by x-ray crystallography to 2 ...

    The p53 tumor suppressor protein binds to DNA as a dimer of dimers to regulate transcription of genes that mediate responses to cellular stress. We have prepared a cross-linked trapped p53 core domain dimer bound to decamer DNA and have determined its structure by x-ray crystallography to 2.3A resolution. The p53 core domain subunits bind nearly symmetrically to opposite faces of the DNA in a head-to-head fashion with a loophelix motif making sequence-specific DNA contacts and bending the DNA by about 20 degrees at the site of protein dimerization. Protein subunit interactions occur over the central DNA minor groove and involve residues from a zinc-binding region. Analysis of tumor derived p53 mutations reveals that the dimerization interface represents a third hot spot for mutation that also includes residues associated with DNA contact and protein stability. Residues associated with p53 dimer formation on DNA are poorly conserved in the p63 and p73 paralogs, possibly contributing to their functional differences. We have used the dimeric protein-DNA complex to model a dimer of p53 dimers bound to icosamer DNA that is consistent with solution bending data and suggests that p53 core domain dimer-dimer contacts are less frequently mutated in human cancer than intra-dimer contacts.


    Organizational Affiliation

    The Wistar Institute, Pennsylvania 19104, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53C [auth A], D [auth B]201Mus musculusMutation(s): 0 
Gene Names: Tp53P53Trp53
Find proteins for P02340 (Mus musculus)
Explore P02340 
Go to UniProtKB:  P02340
NIH Common Fund Data Resources
IMPC:  MGI:98834
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3'A [auth C], B [auth D]16N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TRS
    Query on TRS

    Download Ideal Coordinates CCD File 
    F [auth A], H [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
    C4 H12 N O3
    LENZDBCJOHFCAS-UHFFFAOYSA-O
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    E [auth A], G [auth B]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.30 Å
    • R-Value Free: 0.238 
    • R-Value Work: 0.202 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 44.755α = 90
    b = 94.29β = 90
    c = 119.822γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    HKL-2000data scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2006-05-23
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance