2ADY

Structural Basis of DNA Recognition by p53 Tetramers (complex IV)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Basis of DNA Recognition by p53 Tetramers

Kitayner, M., Rozenberg, H., Kessler, N., Rabinovich, D., Shaulov, L., Haran, T.E., Shakked, Z.

(2006) Mol Cell 22: 741-753

  • DOI: 10.1016/j.molcel.2006.05.015
  • Primary Citation of Related Structures:  
    2ATA, 2AC0, 2ADY, 2AHI

  • PubMed Abstract: 

    • The tumor-suppressor protein p53 is among the most effective of the cell's natural defenses against cancer. In response to cellular stress, p53 binds as a tetramer to diverse DNA targets containing two decameric half-sites, thereby activating the expression of genes involved in cell-cycle arrest or apoptosis ...

    The tumor-suppressor protein p53 is among the most effective of the cell's natural defenses against cancer. In response to cellular stress, p53 binds as a tetramer to diverse DNA targets containing two decameric half-sites, thereby activating the expression of genes involved in cell-cycle arrest or apoptosis. Here we present high-resolution crystal structures of sequence-specific complexes between the core domain of human p53 and different DNA half-sites. In all structures, four p53 molecules self-assemble on two DNA half-sites to form a tetramer that is a dimer of dimers, stabilized by protein-protein and base-stacking interactions. The protein-DNA interface varies as a function of the specific base sequence in correlation with the measured binding affinities of the complexes. The new data establish a structural framework for understanding the mechanisms of specificity, affinity, and cooperativity of DNA binding by p53 and suggest a model for its regulation by regions outside the sequence-specific DNA binding domain.

    Organizational Affiliation: 

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100. Electronic address: zippi.shakked@weizmann.ac.il.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53C [auth A], D [auth B]200Homo sapiensMutation(s): 0 
Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'A [auth E], B [auth F]12N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    		 E [auth A], F [auth B]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.251 
    • R-Value Work: 0.164 
    • R-Value Observed: 0.169 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 91.997α = 90
    b = 67.903β = 92.97
    c = 74.989γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    PDB_EXTRACTdata extraction
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

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    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2006-07-11
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance