7YQK

cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes.

Ai, H.Chu, G.C.Gong, Q.Tong, Z.B.Deng, Z.Liu, X.Yang, F.Xu, Z.Li, J.B.Tian, C.Liu, L.

(2022) J Am Chem Soc 144: 18329-18337

  • DOI: https://doi.org/10.1021/jacs.2c06156
  • Primary Citation of Related Structures:  
    7YQK

  • PubMed Abstract: 

    The chemical synthesis of homogeneously modified histones is a powerful approach to quantitatively decipher how post-translational modifications (PTMs) modulate epigenetic events. Herein, we describe the expedient syntheses of a selection of phosphorylated and ubiquitinated H2AX proteins in a strategy integrating expressed protein hydrazinolysis and auxiliary-mediated protein ligation. These modified H2AX proteins were then used to discover that although H2AXS139 phosphorylation can enhance the binding of the DNA damage repair factor 53BP1 to either an unmodified nucleosome or that bearing a single H2AXK15ub or H4K20me2 modification, it augments 53BP1's binding only weakly to nucleosomes bearing both H2AXK15ub and H4K20me2. To better understand why such a trivalent additive effect is lacking, we solved the cryo-EM structure (3.38 Å) of the complex of 53BP1 with the H2AXK15ub/S139ph_H4K20me2 nucleosome, which showed that H2AXS139 phosphorylation distorts the interaction interface between ubiquitin and 53BP1's UDR motif. Our study revealed that there is redundancy in the interplay of multiple histone PTMs, which may be useful for controlling the dynamic distribution of effector proteins onto nucleosomes bearing different histone variants and PTMs in a time-dependent fashion, through specific cellular biochemical events.


  • Organizational Affiliation

    Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
100Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
83Homo sapiensMutation(s): 0 
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Find proteins for P62805 (Homo sapiens)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AX
C, G
112synthetic constructMutation(s): 0 
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Find proteins for P16104 (Homo sapiens)
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PHAROS:  P16104
GTEx:  ENSG00000188486 
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UniProt GroupP16104
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197903 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-BK [auth O]75Homo sapiensMutation(s): 0 
Gene Names: UBB
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GTEx:  ENSG00000170315 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
UDR motif of 53BP1L [auth K]18Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000067369 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
TP53-binding protein 1M [auth N]118Homo sapiensMutation(s): 0 
Gene Names: TP53BP1
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GTEx:  ENSG00000067369 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)145synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)145synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22137005, 22137005, 81621002, and 21621003 for L. L., 21977090 for J.B. L., and 21825703 for C. T.
The Strategic Priority Research Program of Chinese Academy of SciencesChinaXDB37000000 for C.T.
The China Postdoctoral Science FoundationChina2021M691747 for G. C. C.
The China National Postdoctoral Program for Innovative TalentsChinaBH2340000159 for F.Y.
Special funding from China Postdoctoral Science FoundationChina2022TQ0170 for H.S.A.

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Data collection