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Open data
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Basic information
Entry | Database: PDB / ID: 8j90 | ||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of DDM1-nucleosome complex | ||||||||||||||||||||||||||||||||||||||||||
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![]() | NUCLEAR PROTEIN / Chromatin / Epigenetics / Histon variant / chromatin remodeler | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() DNA-mediated transformation / retrotransposition / chloroplast thylakoid / heterochromatin organization / chromocenter / response to water deprivation / plasmodesma / thylakoid / DNA methylation-dependent heterochromatin formation / plant-type vacuole ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / heterochromatin organization / chromocenter / response to water deprivation / plasmodesma / thylakoid / DNA methylation-dependent heterochromatin formation / plant-type vacuole / ATP-dependent chromatin remodeler activity / plastid / chloroplast stroma / heterochromatin / pericentric heterochromatin / DNA helicase activity / epigenetic regulation of gene expression / chloroplast / heterochromatin formation / structural constituent of chromatin / nucleosome / peroxisome / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / nucleolus / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.71 Å | ||||||||||||||||||||||||||||||||||||||||||
![]() | Osakabe, A. / Takizawa, Y. / Horikoshi, N. / Hatazawa, S. / Berger, F. / Kurumizaka, H. / Kakutani, T. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1. Authors: Akihisa Osakabe / Yoshimasa Takizawa / Naoki Horikoshi / Suguru Hatazawa / Lumi Negishi / Shoko Sato / Frédéric Berger / Tetsuji Kakutani / Hitoshi Kurumizaka / ![]() ![]() 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 ...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. | ||||||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 339.4 KB | Display | ![]() |
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PDB format | ![]() | 252.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 36083MC ![]() 8j91C ![]() 8j92C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 5 types, 9 molecules AEBFCGDHK
#1: Protein | Mass: 15583.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11718.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 16280.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 16756.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | | Mass: 87050.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 51922.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Genus: Escherichia coli / Species: 562 / Description: plasmid DNA amplified by E.coli was used. / Production host: ![]() ![]() |
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#6: DNA chain | Mass: 52424.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Genus: Escherichia coli / Species: 562 / Description: plasmid DNA amplified by E.coli was used. / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: DDM1-nucleosome complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.3 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 10000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34559 / Symmetry type: POINT | ||||||||||||||||||||||||
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