8H1T

Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2022-10-04 Released: 2023-02-01 
  • Deposition Author(s): Ge, W., Yu, C., Xu, R.M.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase.

Ge, W.Yu, C.Li, J.Yu, Z.Li, X.Zhang, Y.Liu, C.P.Li, Y.Tian, C.Zhang, X.Li, G.Zhu, B.Xu, R.M.

(2023) Nature 616: 176-182

  • DOI: https://doi.org/10.1038/s41586-023-05841-y
  • Primary Citation of Related Structures:  
    8H1T

  • PubMed Abstract: 

    Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification 1-3 . The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome 4 , counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1) 5 to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. 6-9 ). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
136Homo sapiensMutation(s): 0 
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Find proteins for P68431 (Homo sapiens)
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo sapiensMutation(s): 0 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-D
C, G
130Homo sapiensMutation(s): 0 
Gene Names: H2AC7H2AFGHIST1H2AD
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Find proteins for P20671 (Homo sapiens)
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PHAROS:  P20671
GTEx:  ENSG00000196866 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-E
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BEH2BFQ
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Find proteins for Q16778 (Homo sapiens)
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GTEx:  ENSG00000184678 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1.4229Homo sapiensMutation(s): 0 
Gene Names: H1-4H1F4HIST1H1E
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GTEx:  ENSG00000168298 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase BAP1729Homo sapiensMutation(s): 1 
Gene Names: BAP1KIAA0272hucep-6
EC: 3.4.19.12
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Find proteins for Q92560 (Homo sapiens)
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GTEx:  ENSG00000163930 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin76Homo sapiensMutation(s): 0 
Gene Names: UBB
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GTEx:  ENSG00000170315 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb group protein ASXL1378Homo sapiensMutation(s): 0 
Gene Names: ASXL1KIAA0978
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Find proteins for Q8IXJ9 (Homo sapiens)
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GTEx:  ENSG00000171456 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (187-MER)187Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (187-MER)187Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTPHENIX1.20

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2019YFA0508900
National Natural Science Foundation of China (NSFC)China31991162
National Natural Science Foundation of China (NSFC)China918532204
National Natural Science Foundation of China (NSFC)China92153302

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-04-19
    Changes: Database references