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Yorodumi- EMDB-28441: Cryo-ET 3D reconstruction of an individual tetra-nucleosome parti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28441 | |||||||||
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Title | Cryo-ET 3D reconstruction of an individual tetra-nucleosome particle in 5 mM NaCl and 20 mM HEPES buffer --- Particle #150 | |||||||||
Map data | Cryo-ET 3D reconstruction of an individual tetra-nucleosome particle in 5 mM NaCl and 20 mM HEPES buffer --- Particle #150 | |||||||||
Sample |
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Keywords | Nucleosome Array / DNA BINDING PROTEIN | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Zhang M / Celis CD / Liu JF / Bustamante C / Ren G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Individual-molecule 3D structures reveal nucleosome array dynamics and regulations Authors: Zhang M / Celis CD / Liu JF / Bustamante C / Ren G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28441.map.gz | 27.8 MB | EMDB map data format | |
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Header (meta data) | emd-28441-v30.xml emd-28441.xml | 7.4 KB 7.4 KB | Display Display | EMDB header |
Images | emd_28441.png | 20.5 KB | ||
Filedesc metadata | emd-28441.cif.gz | 3.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28441 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28441.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-ET 3D reconstruction of an individual tetra-nucleosome particle in 5 mM NaCl and 20 mM HEPES buffer --- Particle #150 | ||||||||||||||||||||
Voxel size | X=Y=Z: 7.4 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Tetranucleosome array
Entire | Name: Tetranucleosome array |
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Components |
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-Supramolecule #1: Tetranucleosome array
Supramolecule | Name: Tetranucleosome array / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 5 mM NaCl 20 mM HEPES 1 mM DTT 1 mM EDTA |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K |
Sectioning | Other: NO SECTIONING |
-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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 5.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: SPIDER / Number images used: 35 |
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-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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