1YCS

P53-53BP2 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2.

Gorina, S.Pavletich, N.P.

(1996) Science 274: 1001-1005

  • DOI: 10.1126/science.274.5289.1001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mutations in the p53 tumor suppressor are among the most frequently observed genetic alterations in human cancer and map to the 200-amino acid core domain of the protein. The core domain contains the sequence-specific DNA binding activity and the in ...

    Mutations in the p53 tumor suppressor are among the most frequently observed genetic alterations in human cancer and map to the 200-amino acid core domain of the protein. The core domain contains the sequence-specific DNA binding activity and the in vitro 53BP2 protein binding activity of p53. The crystal structure of the p53 core domain bound to the 53BP2 protein, which contains an SH3 (Src homology 3) domain and four ankyrin repeats, revealed that (i) the SH3 domain binds the L3 loop of p53 in a manner distinct from that of previously characterized SH3-polyproline peptide complexes, and (ii) an ankyrin repeat, which forms an L-shaped structure consisting of a beta hairpin and two alpha helices, binds the L2 loop of p53. The structure of the complex shows that the 53BP2 binding site on the p53 core domain consists of evolutionarily conserved regions that are frequently mutated in cancer and that it overlaps the site of DNA binding. The six most frequently observed p53 mutations disrupt 53BP2 binding in vitro. The structure provides evidence that the 53BP2-p53 complex forms in vivo and may have a critical role in the p53 pathway of tumor suppression.


    Related Citations: 
    • The P53-Binding Protein 53BP2 Also Interacts with Bcl2 and Impedes Cell Cycle Progression at G2/M
      Naumovski, L., Cleary, M.L.
      (1996) Mol Cell Biol 16: 3884
    • Two Cellular Proteins that Bind to Wild-Type But not Mutant P53
      Iwabuchi, K., Bartel, P.L., Li, B., Marraccino, R., Fields, S.
      (1994) Proc Natl Acad Sci U S A 91: 6098

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P53A199Homo sapiensMutation(s): 0 
Gene Names: RESIDUES 291-529TP53P53
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
53BP2B239Homo sapiensMutation(s): 0 
Gene Names: RESIDUES 291-529TP53BP2ASPP2BBP
Find proteins for Q13625 (Homo sapiens)
Explore Q13625 
Go to UniProtKB:  Q13625
NIH Common Fund Data Resources
PHAROS  Q13625
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
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: 0.286 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.8α = 90
b = 72.8β = 90
c = 119γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
TNTrefinement
X-PLORmodel building
HKLdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-19
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection