+
Open data
-
Basic information
Entry | Database: PDB / ID: 8j90 | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of DDM1-nucleosome complex | ||||||||||||||||||||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||||||||||||||||||||
![]() | NUCLEAR PROTEIN / Chromatin / Epigenetics / Histon variant / chromatin remodeler | ||||||||||||||||||||||||||||||||||||||||||
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 / pericentric heterochromatin / heterochromatin formation / heterochromatin organization / epigenetic regulation of gene expression / DNA helicase activity / chloroplast / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / 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: 4.71 Å | ||||||||||||||||||||||||||||||||||||||||||
![]() | Osakabe, A. / Takizawa, Y. / Horikoshi, N. / Hatazawa, S. / Berger, F. / Kurumizaka, H. / Kakutani, T. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
| ||||||||||||||||||||||||||||||||||||||||||
![]() | ![]() Title: Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1 Authors: Takizawa, Y. / Horikoshi, N. / Hatazawa, S. / Negishi, L. / Sato, S. / Berger, F. / Kakutani, T. / Kurumizaka, H. / Osakabe, A. | ||||||||||||||||||||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 339.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 252.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 80.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36083MC ![]() 8j91C ![]() 8j92C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 5 types, 9 molecules AEBFCGDHK
#1: Protein | Mass: 15583.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11718.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 16280.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 16756.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | | Mass: 87050.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 51922.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Genus: Escherichia coli / Species: 562 / Description: plasmid DNA amplified by E.coli was used. / Production host: ![]() ![]() |
---|---|
#6: DNA chain | Mass: 52424.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Genus: Escherichia coli / Species: 562 / Description: plasmid DNA amplified by E.coli was used. / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: DDM1-nucleosome complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.3 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 10000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-
Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34559 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|