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Yorodumi- EMDB-18474: Subtomogram average of pseudorabies virus nuclear egress complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18474 | ||||||||||||||||||
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Title | Subtomogram average of pseudorabies virus nuclear egress complex (UL31/34) determined in situ | ||||||||||||||||||
Map data | Pseudorabies virus nuclear egress complex determined in situ | ||||||||||||||||||
Sample |
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Keywords | in situ / nuclear egress / VIRAL PROTEIN | ||||||||||||||||||
Biological species | Suid herpesvirus 1 strain Kaplan | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 14.0 Å | ||||||||||||||||||
Authors | Prazak V / Grange M / 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_18474.map.gz | 776.3 KB | EMDB map data format | |
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Header (meta data) | emd-18474-v30.xml emd-18474.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18474_fsc.xml | 2.4 KB | Display | FSC data file |
Images | emd_18474.png | 109.1 KB | ||
Filedesc metadata | emd-18474.cif.gz | 4.6 KB | ||
Others | emd_18474_additional_1.map.gz emd_18474_additional_2.map.gz emd_18474_half_map_1.map.gz emd_18474_half_map_2.map.gz | 14.6 MB 796.7 KB 777.9 KB 777.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18474 | HTTPS FTP |
-Validation report
Summary document | emd_18474_validation.pdf.gz | 684.6 KB | Display | EMDB validaton report |
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Full document | emd_18474_full_validation.pdf.gz | 684.2 KB | Display | |
Data in XML | emd_18474_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | emd_18474_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18474 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18474 | 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_18474.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Pseudorabies virus nuclear egress complex determined in situ | ||||||||||||||||||||
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: #1
File | emd_18474_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: masked, sharpened volume
File | emd_18474_additional_2.map | ||||||||||||
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Annotation | masked, sharpened volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half1
File | emd_18474_half_map_1.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_18474_half_map_2.map | ||||||||||||
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Annotation | half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ
Entire | Name: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ |
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Components |
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-Supramolecule #1: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ
Supramolecule | Name: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Suid herpesvirus 1 strain Kaplan |
-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 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: GIF 2002 |
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 |