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Open data
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Basic information
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Title | Structure of DDM1-nucleosome complex in the apo state | |||||||||
![]() | DDM1-nucleosome complex in the apo state | |||||||||
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Function / homology | ![]() DNA-mediated transformation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Liu Y / Zhang Z / Du J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. Authors: Yue Liu / Zhihui Zhang / Hongmiao Hu / Wei Chen / Fan Zhang / Qian Wang / Changshi Wang / Kaige Yan / Jiamu Du / ![]() ![]() Abstract: Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers. In plants, ...Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeF-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeF-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23 KB 23 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 97.9 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 49.4 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wh5MC ![]() 8wh8C ![]() 8wh9C ![]() 8whaC ![]() 8whbC M: atomic model generated by this map C: citing same article ( |
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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
File | ![]() | ||||||||||||||||||||
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Annotation | DDM1-nucleosome complex in the apo state | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half1 map of DDM1-nucleosome complex in the apo state
File | emd_37529_half_map_1.map | ||||||||||||
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Annotation | Half1 map of DDM1-nucleosome complex in the apo state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map of DDM1-nucleosome complex in the apo state
File | emd_37529_half_map_2.map | ||||||||||||
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Annotation | Half2 map of DDM1-nucleosome complex in the apo state | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : DDM1-nucleosome complex in the apo state
Entire | Name: DDM1-nucleosome complex in the apo state |
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Components |
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-Supramolecule #1: DDM1-nucleosome complex in the apo state
Supramolecule | Name: DDM1-nucleosome complex in the apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 290 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: 15.300968 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RFRPGTVALR EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VAALQEAAEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: ![]() |
-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: 11.436467 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK IFLENVIRDA VTYTEHARRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: ![]() |
-Macromolecule #3: Histone H2A.6
Macromolecule | Name: Histone H2A.6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 13.680854 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MAGRGKTLGS GGAKKATSRS SKAGLQFPVG RIARFLKAGK YAERVGAGAP VYLAAVLEYL AAEVLELAGN AARDNKKTRI VPRHIQLAV RNDEELSKLL GDVTIANGGV MPNIHNLLLP KKAGASKPQE D UniProtKB: Histone H2A.6 |
-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: 16.474459 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MAPRAEKKPA EKKPAAEKPV EEKSKAEKAP AEKKPKAGKK LPKEAGAGGD KKKKMKKKSV ETYKIYIFKV LKQVHPDIGI SSKAMGIMN SFINDIFEKL ASESSKLARY NKKPTITSRE IQTAVRLVLP GELAKHAVSE GTKAVTKFTS S UniProtKB: Histone H2B.6 |
-Macromolecule #7: ATP-dependent DNA helicase DDM1
Macromolecule | Name: ATP-dependent DNA helicase DDM1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 86.844836 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: SMVSLRSRKV IPASEMVSDG KTEKDASGDS PTSVLNEEEN CEEKSVTVVE EEILLAKNGD SSLISEAMAQ EEEQLLKLRE DEEKANNAG SAVAPNLNET QFTKLDELLT QTQLYSEFLL EKMEDITING IESESQKAEP EKTGRGRKRK AASQYNNTKA K RAVAAMIS ...String: SMVSLRSRKV IPASEMVSDG KTEKDASGDS PTSVLNEEEN CEEKSVTVVE EEILLAKNGD SSLISEAMAQ EEEQLLKLRE DEEKANNAG SAVAPNLNET QFTKLDELLT QTQLYSEFLL EKMEDITING IESESQKAEP EKTGRGRKRK AASQYNNTKA K RAVAAMIS RSKEDGETIN SDLTEEETVI KLQNELCPLL TGGQLKSYQL KGVKWLISLW QNGLNGILAD QMGLGKTIQT IG FLSHLKG NGLDGPYLVI APLSTLSNWF NEIARFTPSI NAIIYHGDKN QRDELRRKHM PKTVGPKFPI VITSYEVAMN DAK RILRHY PWKYVVIDEG HRLKNHKCKL LRELKHLKMD NKLLLTGTPL QNNLSELWSL LNFILPDIFT SHDEFESWFD FSEK NKNEA TKEEEEKRRA QVVSKLHGIL RPFILRRMKC DVELSLPRKK EIIMYATMTD HQKKFQEHLV NNTLEAHLGE NAIRG QGWK GKLNNLVIQL RKNCNHPDLL QGQIDGSYLY PPVEEIVGQC GKFRLLERLL VRLFANNHKV LIFSQWTKLL DIMDYY FSE KGFEVCRIDG SVKLDERRRQ IKDFSDEKSS CSIFLLSTRA GGLGINLTAA DTCILYDSDW NPQMDLQAMD RCHRIGQ TK PVHVYRLSTA QSIETRVLKR AYSKLKLEHV VIGQGQFHQE RAKSSTPLEE EDILALLKED ETAEDKLIQT DISDADLD R LLDRSDLTIT APGETQAAEA FPVKGPGWEV VLPSSGGMLS SLNS UniProtKB: ATP-dependent DNA helicase DDM1 |
-Macromolecule #5: DNA (sense strand)
Macromolecule | Name: DNA (sense strand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.310664 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (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) ...String: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (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)(DA)(DA)(DC)(DC)(DG)(DC)(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)(DT)(DC)(DC)(DA)(DG)(DT) (DG)(DC)(DC)(DG)(DG)(DT)(DG) (DT)(DC) (DG)(DC)(DT)(DG)(DA) |
-Macromolecule #6: DNA (antisense strand)
Macromolecule | Name: DNA (antisense strand) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.799977 KDa |
Sequence | String: (DT)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (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) ...String: (DT)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (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)(DG)(DC)(DG)(DG) (DT)(DT)(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)(DG)(DA)(DT) (DT)(DC) (DT)(DC)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 2.2 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 2858 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8wh5: |