1XNI

Tandem Tudor Domain of 53BP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks

Huyen, Y.Zgheib, O.DiTullio Jr., R.A.Gorgoulis, V.G.Zacharatos, P.Petty, T.J.Sheston, E.A.Mellert, H.S.Stavridi, E.S.Halazonetis, T.D.

(2004) Nature 432: 406-411

  • DOI: https://doi.org/10.1038/nature03114
  • Primary Citation of Related Structures:  
    1XNI

  • PubMed Abstract: 

    The mechanisms by which eukaryotic cells sense DNA double-strand breaks (DSBs) in order to initiate checkpoint responses are poorly understood. 53BP1 is a conserved checkpoint protein with properties of a DNA DSB sensor. Here, we solved the structure of the domain of 53BP1 that recruits it to sites of DSBs. This domain consists of two tandem tudor folds with a deep pocket at their interface formed by residues conserved in the budding yeast Rad9 and fission yeast Rhp9/Crb2 orthologues. In vitro, the 53BP1 tandem tudor domain bound histone H3 methylated on Lys 79 using residues that form the walls of the pocket; these residues were also required for recruitment of 53BP1 to DSBs. Suppression of DOT1L, the enzyme that methylates Lys 79 of histone H3, also inhibited recruitment of 53BP1 to DSBs. Because methylation of histone H3 Lys 79 was unaltered in response to DNA damage, we propose that 53BP1 senses DSBs indirectly through changes in higher-order chromatin structure that expose the 53BP1 binding site.


  • Organizational Affiliation

    Wistar Institute, Philadelphia, Pennsylvania 19104-4268, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor suppressor p53-binding protein 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
118Homo sapiensMutation(s): 0 
Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12888 (Homo sapiens)
Explore Q12888 
Go to UniProtKB:  Q12888
PHAROS:  Q12888
GTEx:  ENSG00000067369 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12888
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.61α = 90
b = 157.664β = 90
c = 179.723γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references