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Yorodumi- EMDB-17976: Pseudorabies nuclear C-capsids (US3 KO) vertices determined in situ -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17976 | ||||||||||||||||||||||||
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Title | Pseudorabies nuclear C-capsids (US3 KO) vertices determined in situ | ||||||||||||||||||||||||
Map data | Unfiltered map of nuclear C-capsid vertices | ||||||||||||||||||||||||
Sample |
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Keywords | in situ / nucleus / VIRUS | ||||||||||||||||||||||||
Biological species | Suid herpesvirus 1 strain Kaplan | ||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 24.0 Å | ||||||||||||||||||||||||
Authors | Prazak V / Grange M / Vasishtan D | ||||||||||||||||||||||||
Funding support | United Kingdom, Germany, 7 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_17976.map.gz | 25.1 MB | EMDB map data format | |
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Header (meta data) | emd-17976-v30.xml emd-17976.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17976_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_17976.png | 181.8 KB | ||
Filedesc metadata | emd-17976.cif.gz | 4.1 KB | ||
Others | emd_17976_additional_1.map.gz emd_17976_additional_2.map.gz emd_17976_half_map_1.map.gz emd_17976_half_map_2.map.gz | 25.4 MB 25.4 MB 25.4 MB 25.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17976 | HTTPS FTP |
-Validation report
Summary document | emd_17976_validation.pdf.gz | 983.7 KB | Display | EMDB validaton report |
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Full document | emd_17976_full_validation.pdf.gz | 983.3 KB | Display | |
Data in XML | emd_17976_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_17976_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17976 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17976 | 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_17976.map.gz / Format: CCP4 / Size: 27.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Unfiltered map of nuclear C-capsid vertices | ||||||||||||||||||||
Voxel size | X=Y=Z: 3.55 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sharpened map of nuclear B-capsid vertices
File | emd_17976_additional_1.map | ||||||||||||
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Annotation | Sharpened map of nuclear B-capsid vertices | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered map of nuclear C-capsid vertices
File | emd_17976_additional_2.map | ||||||||||||
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Annotation | Unfiltered map of nuclear C-capsid vertices | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of nuclear C-capsid vertices
File | emd_17976_half_map_1.map | ||||||||||||
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Annotation | Half map of nuclear C-capsid vertices | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of nuclear C-capsid vertices
File | emd_17976_half_map_2.map | ||||||||||||
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Annotation | Half map of nuclear C-capsid vertices | ||||||||||||
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 / 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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Virus shell | Shell ID: 1 / Name: kevin |
-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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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |