6M4D

Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2.

Zhou, M.Dai, L.Li, C.Shi, L.Huang, Y.Guo, Z.Wu, F.Zhu, P.Zhou, Z.

(2021) EMBO J 40: e105907-e105907

  • DOI: https://doi.org/10.15252/embj.2020105907
  • Primary Citation of Related Structures:  
    6M4D, 6M4G, 6M4H

  • PubMed Abstract: 

    Nucleosomes are dynamic entities with wide-ranging compositional variations. Human histone variants H2A.B and H2A.Z.2.2 play critical roles in multiple biological processes by forming unstable nucleosomes and open chromatin structures, but how H2A.B and H2A.Z.2.2 confer these dynamic features to nucleosomes remains unclear. Here, we report cryo-EM structures of nucleosome core particles containing human H2A.B (H2A.B-NCP) at atomic resolution, identifying large-scale structural rearrangements in the histone octamer in H2A.B-NCP. H2A.B-NCP compacts approximately 103 bp of DNA wrapping around the core histones in approximately 1.2 left-handed superhelical turns, in sharp contrast to canonical nucleosome encompassing approximately 1.7 turns of DNA. Micrococcal nuclease digestion assay reveals that nineteen H2A.B-specific residues, including a ROF ("regulating-octamer-folding") sequence of six consecutive residues, are responsible for loosening of H2A.B-NCPs. Unlike H2A.B-NCP, the H2A.Z.2.2-containing nucleosome (Z.2.2-NCP) adopts a less-extended structure and compacts around 125 bp of DNA. Further investigation uncovers a crucial role for the H2A.Z.2.2-specific ROF in both H2A.Z.2.2-NCP opening and SWR1-dependent histone replacement. Taken together, these first high-resolution structure of unstable nucleosomes induced by histone H2A variants elucidate specific functions of H2A.B and H2A.Z.2.2 in enhancing chromatin dynamics.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in 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 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
PHAROS:  P68431
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.V
C, G
114Homo sapiensMutation(s): 0 
Gene Names: H2AFVH2AV
UniProt & NIH Common Fund Data Resources
Find proteins for Q71UI9 (Homo sapiens)
Explore Q71UI9 
Go to UniProtKB:  Q71UI9
PHAROS:  Q71UI9
GTEx:  ENSG00000105968 
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UniProt GroupQ71UI9
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-E
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BEH2BFQ
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens)
Explore Q16778 
Go to UniProtKB:  Q16778
PHAROS:  Q16778
GTEx:  ENSG00000184678 
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UniProt GroupQ16778
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (125-MER)147Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (125-MER)147Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references