8J91

Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.

Osakabe, A.Takizawa, Y.Horikoshi, N.Hatazawa, S.Negishi, L.Sato, S.Berger, F.Kakutani, T.Kurumizaka, H.

(2024) Nat Commun 15: 5187-5187

  • DOI: https://doi.org/10.1038/s41467-024-49465-w
  • Primary Citation of Related Structures:  
    8J90, 8J91, 8J92

  • PubMed Abstract: 

    The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. akihisa-osakabe@g.ecc.u-tokyo.ac.jp.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59226 (Arabidopsis thaliana)
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Go to UniProtKB:  P59226
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UniProt GroupP59226
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59259 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HTA13
C, G
135Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LHQ5 (Arabidopsis thaliana)
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UniProt GroupQ9LHQ5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.6
D, H
153Arabidopsis thalianaMutation(s): 0 
Gene Names: H2B
UniProt
Find proteins for O23629 (Arabidopsis thaliana)
Explore O23629 
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UniProt GroupO23629
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (169-MER)169synthetic construct
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Entity ID: 6
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DNA (169-MER)169synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP21K20628
Japan Society for the Promotion of Science (JSPS)JapanJP22H05172
Japan Society for the Promotion of Science (JSPS)JapanJP22H05178
Japan Science and TechnologyJapanJPMJPR20K3
Japan Society for the Promotion of Science (JSPS)JapanJP22K06098
Japan Society for the Promotion of Science (JSPS)JapanJP18H05534
Japan Society for the Promotion of Science (JSPS)JapanJP20H00449
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121009
Japan Science and TechnologyJapanJPMJER1901
Japan Society for the Promotion of Science (JSPS)Japan21H04977
Japan Society for the Promotion of Science (JSPS)Japan23H00365
Austrian Science FundAustriaP33380
Austrian Science FundAustriaP32054

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Database references