8J90 image
Deposition Date 2023-05-02
Release Date 2024-07-03
Last Version Date 2024-07-24
Entry Detail
PDB ID:
8J90
Keywords:
Title:
Cryo-EM structure of DDM1-nucleosome complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.71 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):HTR2, HTR3, HTR13, HTR9, HTR1
Chain IDs:A, E
Chain Length:139
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):F24B9.25, F24B9.8, F8N16.2, T11P11.4, F16L2_140, F18L15.40, F5K20_30, MTH12.10, MMN10.22
Chain IDs:B, F
Chain Length:106
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:HTA6
Gene (Uniprot):MMN10.22, MMN10_90
Chain IDs:C, G
Chain Length:153
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:HTB9
Gene (Uniprot):H2B
Chain IDs:D, H
Chain Length:153
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (169-MER)
Chain IDs:I
Chain Length:169
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (169-MER)
Chain IDs:J
Chain Length:169
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:ATP-dependent DNA helicase DDM1
Gene (Uniprot):DDM1
Chain IDs:K
Chain Length:767
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Ligand Molecules
Primary Citation
Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun 15 5187 5187 (2024)
PMID: 38992002 DOI: 10.1038/s41467-024-49465-w

Abstact

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.

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Primary Citation of related structures