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Yorodumi- PDB-8j92: Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j92 | ||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W | ||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | NUCLEAR PROTEIN / Chromatin / Epigenetics / Histon variant / chromatin remodeler | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / plastid / chloroplast stroma / heterochromatin / pericentric heterochromatin ...chloroplast thylakoid / chromocenter / response to water deprivation / plasmodesma / plant-type vacuole / thylakoid / plastid / chloroplast stroma / heterochromatin / pericentric heterochromatin / heterochromatin organization / chloroplast / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / protein heterodimerization activity / chromatin binding / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Osakabe, A. / Takizawa, Y. / Horikoshi, N. / Hatazawa, S. / Berger, F. / Kurumizaka, H. / Kakutani, T. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, Austria, 13items
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Citation | Journal: Nat Commun / Year: 2024 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j92.cif.gz | 286.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j92.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 8j92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j92_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8j92_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8j92_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 8j92_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/8j92 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/8j92 | HTTPS FTP |
-Related structure data
Related structure data | 36085MC 8j90C 8j91C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15583.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P59226 #2: Protein | Mass: 11718.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P59259 #3: Protein | Mass: 16280.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FJE8 #4: Protein | Mass: 16756.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: O23629 |
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-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) / Production host: Escherichia coli (E. coli) |
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#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) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.2 MDa / Experimental value: YES | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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: 59.1 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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196430 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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