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Yorodumi- EMDB-18479: Pseudorabies virus cytosolic C-capsid (WT) vertices determined in situ -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18479 | ||||||||||||||||||
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Title | Pseudorabies virus cytosolic C-capsid (WT) vertices determined in situ | ||||||||||||||||||
Map data | Unmasked | ||||||||||||||||||
Sample |
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Keywords | Capsid / capsid vertex specific component / in situ / virus | ||||||||||||||||||
Biological species | Suid herpesvirus 1 strain Kaplan | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 26.0 Å | ||||||||||||||||||
Authors | Mironova Y / Prazak V / Vasishtan D | ||||||||||||||||||
Funding support | United Kingdom, Germany, 5 items
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Citation | Journal: To Be Published Title: NECing goes: flexibility of the herpesvirus nuclear egress complex Authors: Prazak V / Mironova Y / Vasishtan D / Hagen C / Laugks U / Jensen Y / Sanders S / Heumann JM / Bosse JB / Klupp B / Mettenleiter TC / Grange M / Grunewald K | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18479.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-18479-v30.xml emd-18479.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18479_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_18479.png | 68.4 KB | ||
Filedesc metadata | emd-18479.cif.gz | 4.5 KB | ||
Others | emd_18479_additional_1.map.gz emd_18479_half_map_1.map.gz emd_18479_half_map_2.map.gz | 3.2 MB 3.2 MB 3.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18479 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18479 | HTTPS FTP |
-Validation report
Summary document | emd_18479_validation.pdf.gz | 799.8 KB | Display | EMDB validaton report |
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Full document | emd_18479_full_validation.pdf.gz | 799.4 KB | Display | |
Data in XML | emd_18479_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | emd_18479_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18479 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18479 | 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_18479.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Unmasked | ||||||||||||||||||||
Voxel size | X=Y=Z: 7.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sub-tomogram average of the cytosolic A-capsid
File | emd_18479_additional_1.map | ||||||||||||
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Annotation | Sub-tomogram average of the cytosolic A-capsid | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered
File | emd_18479_half_map_1.map | ||||||||||||
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Annotation | Unfiltered | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered
File | emd_18479_half_map_2.map | ||||||||||||
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Annotation | Unfiltered | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Suid herpesvirus 1 strain Kaplan
Entire | Name: Suid herpesvirus 1 strain Kaplan |
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Components |
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-Supramolecule #1: Suid herpesvirus 1 strain Kaplan
Supramolecule | Name: Suid herpesvirus 1 strain Kaplan / type: virus / ID: 1 / Parent: 0 / Details: Cells were infected with wt PrV (Kaplan) for 10h / NCBI-ID: 33703 / Sci species name: Suid herpesvirus 1 strain Kaplan / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 200 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 310.15 K / Instrument: LEICA EM GP Details: Vitrified samples were milled using dual beam cryo-FIB-SEM (Aquilos). |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.4 sec. / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 26000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |