7CMZ

Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

PHF8-promoted TOPBP1 demethylation drives ATR activation and preserves genome stability.

Ma, S.Cao, C.Che, S.Wang, Y.Su, D.Liu, S.Gong, W.Liu, L.Sun, J.Zhao, J.Wang, Q.Song, N.Ge, T.Guo, Q.Tian, S.Chen, C.D.Zhang, T.Wang, J.Ding, X.Yang, F.Ying, G.Yang, J.Zhang, K.Zhu, Y.Yao, Z.Yang, N.Shi, L.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf7684
  • Primary Citation of Related Structures:  
    7CMZ

  • PubMed Abstract: 

    The checkpoint kinase ATR [ATM (ataxia-telangiectasia mutated) and rad3-related] is a master regulator of DNA damage response. Yet, how ATR activity is regulated remains to be investigated. We report here that histone demethylase PHF8 (plant homeodomain finger protein 8) plays a key role in ATR activation and replication stress response. Mechanistically, PHF8 interacts with and demethylates TOPBP1 (DNA topoisomerase 2-binding protein 1), an essential allosteric activator of ATR, under unperturbed conditions, but replication stress results in PHF8 phosphorylation and dissociation from TOPBP1. Consequently, hypomethylated TOPBP1 facilitates RAD9 (RADiation sensitive 9) binding and chromatin loading of the TOPBP1-RAD9 complex to fully activate ATR and thus safeguard the genome and protect cells against replication stress. Our study uncovers a demethylation and phosphorylation code that controls the assembly of TOPBP1-scaffolded protein complex, and provides molecular insight into non-histone methylation switch in ATR activation.


  • Organizational Affiliation

    State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2-binding protein 1230Homo sapiensMutation(s): 0 
Gene Names: TOPBP1KIAA0259
UniProt & NIH Common Fund Data Resources
Find proteins for Q92547 (Homo sapiens)
Explore Q92547 
Go to UniProtKB:  Q92547
PHAROS:  Q92547
GTEx:  ENSG00000163781 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92547
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone lysine demethylase PHF822Homo sapiensMutation(s): 0 
EC: 1.14.11.27 (PDB Primary Data), 1.14.11.65 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPP1 (Homo sapiens)
Explore Q9UPP1 
Go to UniProtKB:  Q9UPP1
PHAROS:  Q9UPP1
GTEx:  ENSG00000172943 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPP1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.517α = 90
b = 60.35β = 90
c = 66.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81972660
National Natural Science Foundation of China (NSFC)China31671474
Ministry of Science and Technology (MoST, China)China2018YFA0107004
Ministry of Science and Technology (MoST, China)China2019YFA0508902

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary