6M4G

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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: 10.15252/embj.2020105907
  • Primary Citation of Related Structures:  
    6M4H, 6M4G, 6M4D

  • 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 ...

    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

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1C [auth A], F [auth E]136Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B], G [auth F]103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 2-EE [auth D], H126Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BEH2BFQH2BC21
Find proteins for Q16778 (Homo sapiens)
Explore Q16778 
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PHAROS:  Q16778
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A-Bbd type 2/3I [auth C], J [auth G]115Homo sapiensMutation(s): 0 
Gene Names: H2AB2H2AFB2H2AB3H2ABBDH2AFBH2AFB3
Find proteins for P0C5Z0 (Homo sapiens)
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (93-MER)A [auth I]147Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (93-MER)B [auth J]147Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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