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- EMDB-36084: Cryo-EM structure of nucleosome containing Arabidopsis thaliana h... -
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Open data
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Basic information
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Title | Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones | ||||||||||||||||||||||||||||||||||||||||||
![]() | Cryo-EM map of nucleosome containing Arabidopsis thaliana histones | ||||||||||||||||||||||||||||||||||||||||||
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![]() | Chromatin / Epigenetics / Histon variant / chromatin remodeler / NUCLEAR PROTEIN | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / thylakoid / plant-type vacuole / plastid / chloroplast stroma / chloroplast / structural constituent of chromatin ...chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / thylakoid / plant-type vacuole / plastid / chloroplast stroma / chloroplast / structural constituent of chromatin / nucleosome / peroxisome / protein heterodimerization activity / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.7 KB 25.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.1 KB | Display | ![]() |
Images | ![]() | 120.4 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 26.7 MB 23.4 MB 23.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j91MC ![]() 8j90C ![]() 8j92C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM map of nucleosome containing Arabidopsis thaliana histones | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Cryo-EM map of nucleosome containing Arabidopsis thaliana histones...
File | emd_36084_additional_1.map | ||||||||||||
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Annotation | Cryo-EM map of nucleosome containing Arabidopsis thaliana histones post-processed by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36084_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36084_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nucleosome containing Arabidopsis thaliana histones
Entire | Name: Nucleosome containing Arabidopsis thaliana histones |
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Components |
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-Supramolecule #1: Nucleosome containing Arabidopsis thaliana histones
Supramolecule | Name: Nucleosome containing Arabidopsis thaliana histones / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.583246 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRFRPGTV ALREIRKYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVAALQEA AEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.718744 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKIFLENVI RDAVTYTEHA RRKTVTAMD VVYALKRQGR TLYGFGG UniProtKB: Histone H4 |
-Macromolecule #3: HTA13
Macromolecule | Name: HTA13 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.154316 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMAGRGKT LGSGVAKKST SRSSKAGLQF PVGRIARFLK NGKYATRVGA GAPVYLAAVL EYLAAEVLEL AGNAARDNKK TRIVPRHIQ LAVRNDEELS KLLGDVTIAN GGVMPNIHSL LLPKKAGASK PSADED UniProtKB: Probable histone H2A.2 |
-Macromolecule #4: Histone H2B.6
Macromolecule | Name: Histone H2B.6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.756738 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMAPRAEK KPAEKKPAAE KPVEEKSKAE KAPAEKKPKA GKKLPKEAGA GGDKKKKMKK KSVETYKIYI FKVLKQVHPD IGISSKAMG IMNSFINDIF EKLASESSKL ARYNKKPTIT SREIQTAVRL VLPGELAKHA VSEGTKAVTK FTSS UniProtKB: Histone H2B.6 |
-Macromolecule #5: DNA (169-MER)
Macromolecule | Name: DNA (169-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.922059 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC) ...String: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG) (DC)(DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT)(DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC) (DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT) (DA)(DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT) |
-Macromolecule #6: DNA (169-MER)
Macromolecule | Name: DNA (169-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 52.424352 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG)(DC)(DT) (DC)(DG)(DC)(DG)(DA)(DT)(DA) (DG)(DG) (DG)(DT)(DC)(DC)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 10.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |