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Open data
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Basic information
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Title | Structure of DDM1-nucleosome complex in ADP-BeFx state | |||||||||
![]() | DDM1-nucleosome complex in the ADP-BeFx state | |||||||||
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![]() | complex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex / GENE REGULATION | |||||||||
Function / homology | ![]() DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / : / response to water deprivation / plasmodesma / plant-type vacuole / DNA methylation-dependent heterochromatin formation / thylakoid ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / : / response to water deprivation / plasmodesma / plant-type vacuole / DNA methylation-dependent heterochromatin formation / thylakoid / ATP-dependent chromatin remodeler activity / plastid / chloroplast stroma / heterochromatin formation / epigenetic regulation of gene expression / DNA helicase activity / chloroplast / response to bacterium / response to wounding / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / DNA helicase / chromatin remodeling / protein heterodimerization activity / nucleolus / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 Å | |||||||||
![]() | 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 | ![]() | 6.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.5 KB 23.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 101 KB | ||
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() | 49.5 MB 49.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 685.1 KB | Display | ![]() |
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Full document | ![]() | 684.6 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wh9MC ![]() 8wh5C ![]() 8wh8C ![]() 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 ADP-BeFx 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 ADP-BeFx state
File | emd_37535_half_map_1.map | ||||||||||||
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Annotation | Half1 map of DDM1-nucleosome complex in the ADP-BeFx state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map of DDM1-nucleosome complex in the ADP-BeFx state
File | emd_37535_half_map_2.map | ||||||||||||
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Annotation | Half2 map of DDM1-nucleosome complex in the ADP-BeFx state | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : DDM1-nucleosome complex in ADP-BeFx state
+Supramolecule #1: DDM1-nucleosome complex in ADP-BeFx state
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A.6
+Macromolecule #4: Histone H2B.6
+Macromolecule #7: ATP-dependent DNA helicase DDM1
+Macromolecule #5: DNA (sense strand)
+Macromolecule #6: DNA (antisense strand)
+Macromolecule #8: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 6776 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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-8wh9: |