5Z78

Structure of TIRR/53BP1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for recognition of 53BP1 tandem Tudor domain by TIRR

Dai, Y.Zhang, A.Shan, S.Gong, Z.Zhou, Z.

(2018) Nat Commun 9: 2123-2123

  • DOI: 10.1038/s41467-018-04557-2
  • Primary Citation of Related Structures:  
    5Z78

  • PubMed Abstract: 
  • P53-binding protein 1 (53BP1) regulates the double-strand break (DSB) repair pathway choice. A recently identified 53BP1-binding protein Tudor-interacting repair regulator (TIRR) modulates the access of 53BP1 to DSBs by masking the H4K20me2 binding surface on 53BP1, but the underlying mechanism remains unclear ...

    P53-binding protein 1 (53BP1) regulates the double-strand break (DSB) repair pathway choice. A recently identified 53BP1-binding protein Tudor-interacting repair regulator (TIRR) modulates the access of 53BP1 to DSBs by masking the H4K20me2 binding surface on 53BP1, but the underlying mechanism remains unclear. Here we report the 1.76-Å crystal structure of TIRR in complex with 53BP1 tandem Tudor domain. We demonstrate that the N-terminal region (residues 10-24) and the L8-loop of TIRR interact with 53BP1 Tudor through three loops (L1, L3, and L1'). TIRR recognition blocks H4K20me2 binding to 53BP1 Tudor and modulates 53BP1 functions in vivo. Structure comparisons identify a TIRR histidine (H106) that is absent from the TIRR homolog Nudt16, but essential for 53BP1 Tudor binding. Remarkably, mutations mimicking TIRR binding modules restore the disrupted binding of Nudt16-53BP1 Tudor. Our studies elucidate the mechanism by which TIRR recognizes 53BP1 Tudor and functions as a cellular inhibitor of the histone methyl-lysine readers.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, 100049, China. zhouzh@sun5.ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tudor-interacting repair regulator proteinB [auth A], A [auth B]209Mus musculusMutation(s): 0 
Gene Names: Nudt16l1SdosTirr
UniProt
Find proteins for Q8VHN8 (Mus musculus)
Explore Q8VHN8 
Go to UniProtKB:  Q8VHN8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TP53-binding protein 1C123Homo 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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.108α = 90
b = 167.108β = 90
c = 46.505γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-27 
  • Released Date: 2018-06-06 
  • Deposition Author(s): Dai, Y.X., Shan, S.

Funding OrganizationLocationGrant Number
Chinese Ministry of Science and TechnologyChina2015CB856200

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references