1TUP

TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


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


Literature

Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations.

Cho, Y., Gorina, S., Jeffrey, P.D., Pavletich, N.P.

(1994) Science 265: 346-355

  • DOI: 10.1126/science.8023157
  • Primary Citation of Related Structures:  
    1TSR, 1TUP

  • PubMed Abstract: 

    • Mutations in the p53 tumor suppressor are the most frequently observed genetic alterations in human cancer. The majority of the mutations occur in the core domain which contains the sequence-specific DNA binding activity of the p53 protein (residues ...

    Mutations in the p53 tumor suppressor are the most frequently observed genetic alterations in human cancer. The majority of the mutations occur in the core domain which contains the sequence-specific DNA binding activity of the p53 protein (residues 102-292), and they result in loss of DNA binding. The crystal structure of a complex containing the core domain of human p53 and a DNA binding site has been determined at 2.2 angstroms resolution and refined to a crystallographic R factor of 20.5 percent. The core domain structure consists of a beta sandwich that serves as a scaffold for two large loops and a loop-sheet-helix motif. The two loops, which are held together in part by a tetrahedrally coordinated zinc atom, and the loop-sheet-helix motif form the DNA binding surface of p53. Residues from the loop-sheet-helix motif interact in the major groove of the DNA, while an arginine from one of the two large loops interacts in the minor groove. The loops and the loop-sheet-helix motif consist of the conserved regions of the core domain and contain the majority of the p53 mutations identified in tumors. The structure supports the hypothesis that DNA binding is critical for the biological activity of p53, and provides a framework for understanding how mutations inactivate it.

    Related Citations: 
    • The DNA-Binding Domain of P53 Contains the Four Conserved Regions and the Major Mutation Hot Spots
      Pavletich, N.P., Chambers, K.A., Pabo, C.O.
      (1993) Genes Dev 7: 2556
    • P53 Function and Dysfunction
      Vogelstein, B., Kinzler, K.W.
      (1992) Cell 70: 523
    Organizational Affiliation: 

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (P53 TUMOR SUPPRESSOR )A, B, C219Homo sapiensMutation(s): 0 
Gene Names: TP53, P53
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637
GTEx  ENSG00000141510
Protein Feature View
Expand
  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3')E21N/A
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3')F21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.5α = 90
b = 67.9β = 105.5
c = 108.8γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance