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Yorodumi- EMDB-1320: Direct visualization of the putative portal in the Kaposi's sarco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1320 | |||||||||
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Title | Direct visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography. | |||||||||
Map data | This is a MRC density map averaged from KSHV A-capsid tomograms. 5-fold symmetry is applied along the unique vertex. | |||||||||
Sample |
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Biological species | Human herpesvirus 8 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 40.0 Å | |||||||||
Authors | Deng B / O'Connor CM / Kedes DH / Zhou ZH | |||||||||
Citation | Journal: J Virol / Year: 2007 Title: Direct visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography. Authors: Binbin Deng / Christine M O'Connor / Dean H Kedes / Z Hong Zhou / Abstract: Genetic and biochemical studies have suggested the existence of a bacteriophage-like, DNA-packaging/ejecting portal complex in herpesviruses capsids, but its arrangement remained unknown. Here, we ...Genetic and biochemical studies have suggested the existence of a bacteriophage-like, DNA-packaging/ejecting portal complex in herpesviruses capsids, but its arrangement remained unknown. Here, we report the first visualization of a unique vertex in the Kaposi's sarcoma-associated herpesvirus (KSHV) capsid by cryoelectron tomography, thus providing direct structural evidence for the existence of a portal complex in a gammaherpesvirus. This putative KSHV portal is an internally localized, umbilicated structure and lacks all of the external machineries characteristic of portals in DNA bacteriophages. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1320.map.gz | 16.7 MB | EMDB map data format | |
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Header (meta data) | emd-1320-v30.xml emd-1320.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | 1320.gif emd_1320.tif emd_1320_1.tif emd_1320_2.tif emd_1320_3.tif | 46.1 KB 2.3 MB 2.3 MB 2.3 MB 2.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1320 | HTTPS FTP |
-Validation report
Summary document | emd_1320_validation.pdf.gz | 284.7 KB | Display | EMDB validaton report |
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Full document | emd_1320_full_validation.pdf.gz | 283.8 KB | Display | |
Data in XML | emd_1320_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1320 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1320 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1320.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a MRC density map averaged from KSHV A-capsid tomograms. 5-fold symmetry is applied along the unique vertex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.858 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : KSHV
Entire | Name: KSHV |
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Components |
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-Supramolecule #1000: KSHV
Supramolecule | Name: KSHV / type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 1 |
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-Supramolecule #1: Human herpesvirus 8
Supramolecule | Name: Human herpesvirus 8 / type: virus / ID: 1 / Name.synonym: Kaposis sarcoma-associated herpesvirus / NCBI-ID: 37296 / Sci species name: Human herpesvirus 8 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Kaposis sarcoma-associated herpesvirus |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Grid | Details: holey carbon 300 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: Blot for 1 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 90 K / Max: 90 K / Average: 90 K |
Details | Tilted from -70 to +70 with 2 degree interval. |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 23000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 70 ° / Tilt series - Axis1 - Max angle: 70 ° |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: PROJALIGN |
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