7XD0

cryo-EM structure of H2BK34ub nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity.

Ai, H.Sun, M.Liu, A.Sun, Z.Liu, T.Cao, L.Liang, L.Qu, Q.Li, Z.Deng, Z.Tong, Z.Chu, G.Tian, X.Deng, H.Zhao, S.Li, J.B.Lou, Z.Liu, L.

(2022) Nat Chem Biol 18: 972-980

  • DOI: https://doi.org/10.1038/s41589-022-01067-7
  • Primary Citation of Related Structures:  
    7XCR, 7XCT, 7XD0, 7XD1

  • PubMed Abstract: 

    Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the central focus. Here our study on the crosstalk between H2BK34ub and Dot1L-catalyzed H3K79me suggests a novel mechanism of ubiquitination-induced nucleosome distortion to stimulate the activity of an enzyme. We determined the cryo-electron microscopy structures of Dot1L-H2BK34ub nucleosome complex and the H2BK34ub nucleosome alone. The structures reveal that H2BK34ub induces an almost identical orientation and binding pattern of Dot1L on nucleosome as H2BK120ub, which positions Dot1L for the productive conformation through direct ubiquitin-enzyme contacts. However, H2BK34-anchored ubiquitin does not directly interact with Dot1L as occurs in the case of H2BK120ub, but rather induces DNA and histone distortion around the modified site. Our findings establish the structural framework for understanding the H2BK34ub-H3K79me trans-crosstalk and highlight the diversity of mechanisms for histone ubiquitination to activate chromatin-modifying enzymes.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China. louzy@mail.tsinghua.edu.cn.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4A [auth F],
H [auth B]
83Homo sapiensMutation(s): 0 
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AB [auth G],
G [auth C]
108Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABHIST1H2AEhCG_1640984hCG_1787383
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KC [auth H],
F [auth D]
92synthetic constructMutation(s): 0 
UniProt
Find proteins for Q2M2T1 (Bos taurus)
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UniProt GroupQ2M2T1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone domain-containing proteinD [auth E],
E [auth A]
99Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40K [auth L],
L [auth K]
76synthetic constructMutation(s): 0 
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Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (146-MER)146synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (146-MER)146synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private2017YFA0505200
National Natural Science Foundation of China (NSFC)China21977090
National Natural Science Foundation of China (NSFC)China21532004
National Natural Science Foundation of China (NSFC)China91753205
National Natural Science Foundation of China (NSFC)China81621002
National Natural Science Foundation of China (NSFC)China32122024
National Natural Science Foundation of China (NSFC)China22137005

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 2.0: 2022-06-08
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2022-07-06
    Changes: Database references
  • Version 2.2: 2022-09-07
    Changes: Database references