8SVF

BAP1/ASXL1 bound to the H2AK119Ub Nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental, integrative
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.

Thomas, J.F.Valencia-Sanchez, M.I.Tamburri, S.Gloor, S.L.Rustichelli, S.Godinez-Lopez, V.De Ioannes, P.Lee, R.Abini-Agbomson, S.Gretarsson, K.Burg, J.M.Hickman, A.R.Sun, L.Gopinath, S.Taylor, H.F.Sun, Z.W.Ezell, R.J.Vaidya, A.Meiners, M.J.Cheek, M.A.Rice, W.J.Svetlov, V.Nudler, E.Lu, C.Keogh, M.C.Pasini, D.Armache, K.J.

(2023) Sci Adv 9: eadg9832-eadg9832

  • DOI: https://doi.org/10.1126/sciadv.adg9832
  • Primary Citation of Related Structures:  
    8SVF

  • PubMed Abstract: 

    Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. The PR-DUB subunits (BAP1 and ASXL1) are among the most frequently mutated epigenetic factors in human cancers. How PR-DUB establishes specificity for H2AK119Ub over other nucleosomal ubiquitination sites and how disease-associated mutations of the enzyme affect activity are unclear. Here, we determine a cryo-EM structure of human BAP1 and the ASXL1 DEUBAD in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for restructuring the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing insight into understanding cancer etiology.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
136Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
130Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
126Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase BAP1729Homo sapiensMutation(s): 0 
Gene Names: BAP1KIAA0272hucep-6
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q92560 (Homo sapiens)
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PHAROS:  Q92560
GTEx:  ENSG00000163930 
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UniProt GroupQ92560
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb group protein ASXL11,541Homo sapiensMutation(s): 0 
Gene Names: ASXL1KIAA0978
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PHAROS:  Q8IXJ9
GTEx:  ENSG00000171456 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin76Homo sapiensMutation(s): 0 
Gene Names: UBC
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Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA/RNA (187-MER)187synthetic construct
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA/RNA (327-MER)327synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.1
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115882
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA266978
The Mark FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Refinement description, Source and taxonomy