+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39292 | |||||||||||||||
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Title | 5-fold block of DNA-Full medusavirus capsid | |||||||||||||||
Map data | 5-fold block of DNA-Full medusavirus capsid | |||||||||||||||
Sample |
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Keywords | Giant virus / NCLDV / Icosahedral / VIRUS | |||||||||||||||
Biological species | Acanthamoeba castellanii medusavirus | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.32 Å | |||||||||||||||
Authors | Murata K / Song C / Watanabe R | |||||||||||||||
Funding support | Japan, 4 items
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Citation | Journal: To Be Published Title: Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy Authors: Watanabe R / Song C / Takemura M / Murata K | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39292.map.gz | 22.9 MB | EMDB map data format | |
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Header (meta data) | emd-39292-v30.xml emd-39292.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39292_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_39292.png | 123.4 KB | ||
Filedesc metadata | emd-39292.cif.gz | 4.1 KB | ||
Others | emd_39292_half_map_1.map.gz emd_39292_half_map_2.map.gz | 49.4 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39292 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39292 | HTTPS FTP |
-Validation report
Summary document | emd_39292_validation.pdf.gz | 1013.9 KB | Display | EMDB validaton report |
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Full document | emd_39292_full_validation.pdf.gz | 1013.5 KB | Display | |
Data in XML | emd_39292_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_39292_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39292 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39292 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_39292.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 5-fold block of DNA-Full medusavirus capsid | ||||||||||||||||||||
Voxel size | X=Y=Z: 3.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_39292_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39292_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Acanthamoeba castellanii medusavirus
Entire | Name: Acanthamoeba castellanii medusavirus |
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Components |
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-Supramolecule #1: Acanthamoeba castellanii medusavirus
Supramolecule | Name: Acanthamoeba castellanii medusavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2080449 / Sci species name: Acanthamoeba castellanii medusavirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Acanthamoeba castellanii (eukaryote) |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 260.0 Å / T number (triangulation number): 277 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 76.0 K / Max: 77.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number real images: 2084 / Average exposure time: 3.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |