8WG5

Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 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

Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16.

Ai, H.He, Z.Deng, Z.Chu, G.C.Shi, Q.Tong, Z.Li, J.B.Pan, M.Liu, L.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01342-2
  • Primary Citation of Related Structures:  
    8WG5

  • PubMed Abstract: 

    Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in transcription repression, is dynamically regulated by the opposing activities of Polycomb repressive complex 1 (PRC1) and nucleosome deubiquitinases including the primary human USP16 and Polycomb repressive deubiquitinase (PR-DUB) complex. Recently, the catalytic mechanism for the multi-subunit PR-DUB complex has been described, but how the single-subunit USP16 recognizes the H2AK119Ub nucleosome and cleaves the ubiquitin (Ub) remains unknown. Here we report the cryo-EM structure of USP16-H2AK119Ub nucleosome complex, which unveils a fundamentally distinct mode of H2AK119Ub deubiquitination compared to PR-DUB, encompassing the nucleosome recognition pattern independent of the H2A-H2B acidic patch and the conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail. Our work highlights the mechanism diversity of H2AK119Ub deubiquitination and provides a structural framework for understanding the disease-causing mutations of USP16.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 16A [auth M]823Homo sapiensMutation(s): 0 
Gene Names: USP16MSTP039
EC: 3.4.19.12
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PHAROS:  Q9Y5T5
GTEx:  ENSG00000156256 
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UniProt GroupQ9Y5T5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1B [auth A],
F [auth E]
98Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth B],
G [auth F]
79Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP62805
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/ED [auth C],
H [auth G]
111Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KE [auth D],
I [auth H]
94Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
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GTEx:  ENSG00000197903 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin BL [auth U]76Homo sapiensMutation(s): 0 
Gene Names: UBB
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GTEx:  ENSG00000170315 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)J [auth I]147Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (147-MER)K [auth J]147Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 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, 92253302, 22227810 for L. Liu, and 22277073 for M. Pan

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references