7M1X

Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis of chromatin regulation by histone variant H2A.Z.

Lewis, T.S.Sokolova, V.Jung, H.Ng, H.Tan, D.

(2021) Nucleic Acids Res 49: 11379-11391

  • DOI: https://doi.org/10.1093/nar/gkab907
  • Primary Citation of Related Structures:  
    7M1X

  • PubMed Abstract: 

    The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an activating and a repressive role of H2A.Z in transcription. Here we report cryo-electron microscopy (cryo-EM) structures of nucleosomes and chromatin fibers containing H2A.Z and those containing canonical H2A. The structures show that H2A.Z incorporation results in substantial structural changes in both nucleosome and chromatin fiber. While H2A.Z increases the mobility of DNA terminus in nucleosomes, it simultaneously enables nucleosome arrays to form a more regular and condensed chromatin fiber. We also demonstrated that H2A.Z's ability to enhance nucleosomal DNA mobility is largely attributed to its characteristic shorter C-terminus. Our study provides the structural basis for H2A.Z-mediated chromatin regulation, showing that the increase flexibility of the DNA termini in H2A.Z nucleosomes is central to its dual-functions in chromatin regulation and in transcription.


  • Organizational Affiliation

    Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY 11794, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E]
136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
UniProt
Find proteins for P02302 (Xenopus laevis)
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Go to UniProtKB:  P02302
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UniProt GroupP02302
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.ZE [auth C],
I [auth G]
128Mus musculusMutation(s): 0 
Gene Names: H2az1H2afzH2az
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S6 (Mus musculus)
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Go to UniProtKB:  P0C0S6
IMPC:  MGI:1888388
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UniProt GroupP0C0S6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1F [auth D],
J [auth H]
126Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (136-MER)A [auth I]147unidentified
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (136-MER)B [auth J]147unidentified
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIX1.15.2

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 States1R35GM133611
National Science Foundation (NSF, United States)United States1942049

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Database references
  • Version 1.2: 2021-11-17
    Changes: Database references