+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37535 | |||||||||
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Title | Structure of DDM1-nucleosome complex in ADP-BeFx state | |||||||||
Map data | DDM1-nucleosome complex in the ADP-BeFx state | |||||||||
Sample |
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Keywords | complex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex / GENE REGULATION | |||||||||
Function / homology | Function and homology information DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / DNA methylation-dependent heterochromatin formation / ATP-dependent chromatin remodeler activity ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / DNA methylation-dependent heterochromatin formation / 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 / peroxisome / structural constituent of chromatin / nucleosome / 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 | Arabidopsis thaliana (thale cress) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 Å | |||||||||
Authors | Liu Y / Zhang Z / Du J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Plants / Year: 2024 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 | emd_37535.map.gz | 6.4 MB | EMDB map data format | |
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Header (meta data) | emd-37535-v30.xml emd-37535.xml | 23.5 KB 23.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37535_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_37535.png | 101 KB | ||
Filedesc metadata | emd-37535.cif.gz | 7.4 KB | ||
Others | emd_37535_half_map_1.map.gz emd_37535_half_map_2.map.gz | 49.5 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37535 | HTTPS FTP |
-Related structure data
Related structure data | 8wh9MC 8wh5C 8wh8C 8whaC 8whbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37535.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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 |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8wh9: |