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- PDB-8wha: Structure of DDM1-nucleosome complex in the ADP-BeFx state with D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wha | ||||||
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Title | Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 | ||||||
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![]() | GENE REGULATION / complex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex | ||||||
Function / homology | ![]() DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / thylakoid / DNA methylation-dependent heterochromatin formation / plant-type vacuole / ATP-dependent chromatin remodeler activity ...DNA-mediated transformation / retrotransposition / chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / thylakoid / DNA methylation-dependent heterochromatin formation / plant-type vacuole / ATP-dependent chromatin remodeler activity / plastid / chloroplast stroma / DNA helicase activity / epigenetic regulation of gene expression / chloroplast / response to bacterium / heterochromatin formation / response to wounding / structural constituent of chromatin / nucleosome / peroxisome / 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 450.5 KB | Display | ![]() |
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PDB format | ![]() | 346.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37537MC ![]() 8wh5C ![]() 8wh8C ![]() 8wh9C ![]() 8whbC 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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1 |
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Components
-Protein , 5 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15300.968 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HTR2, At1g09200, T12M4.9, HTR3, At3g27360, K1G2.8, HTR13, At5g10390, F12B17_260, HTR9, At5g10400, F12B17_250, HTR1, At5g65360, MNA5.9 Production host: ![]() ![]() #2: Protein | Mass: 11436.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: At1g07660, F24B9.25, At1g07820, F24B9.8, At2g28740, F8N16.2, T11P11.4, At3g45930, F16L2_140, At3g46320, F18L15.40, At3g53730, F5K20_30, At5g59690, MTH12.10, At5g59970, MMN10.22 Production host: ![]() ![]() #3: Protein | Mass: 13680.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 16474.459 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | Mass: 86844.836 Da / Num. of mol.: 2 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: 45123.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 45626.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 4 molecules ![](data/chem/img/BEF.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#8: Chemical | #9: Chemical | |
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-Details
Has ligand of interest | Y |
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-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 in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Molecular weight | Value: 0.376 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6776 |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
EM software | Name: RELION / Version: 3.1 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 3898721 |
3D reconstruction | Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24191 / Symmetry type: POINT |
Atomic model building | Space: REAL |