3EXL

Crystal Structure of a p53 Core Tetramer Bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

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


Literature

Crystal structure of a p53 core tetramer bound to DNA.

Malecka, K.A., Ho, W.C., Marmorstein, R.

(2009) Oncogene 28: 325-333

  • DOI: 10.1038/onc.2008.400
  • Primary Citation of Related Structures:  
    3EXJ, 3EXL

  • PubMed Abstract: 

    • The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex ...

    The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

    Organizational Affiliation: 

    The Wistar Institute, Philadelphia, PA 19104, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mouse p53 core domainA197Mus musculusMutation(s): 0 
Gene Names: Tp53, P53, Trp53
UniProt & NIH Common Fund Data Resources
Find proteins for P02340 (Mus musculus)
Explore P02340 
Go to UniProtKB:  P02340
IMPC:  MGI:98834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02340
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'B [auth C]11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'C [auth D]12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC
Download Ideal Coordinates CCD File 
D [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.418α = 90
b = 68.103β = 104.18
c = 34.428γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description