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Yorodumi- EMDB-20431: Kaposi's sarcoma-associated herpesvirus (KSHV), C1 portal vertex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20431 | |||||||||||||||||||||||||||||||||||||||||||||
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Title | Kaposi's sarcoma-associated herpesvirus (KSHV), C1 portal vertex reconstruction | |||||||||||||||||||||||||||||||||||||||||||||
Map data | None | |||||||||||||||||||||||||||||||||||||||||||||
Sample |
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Biological species | Human gammaherpesvirus 8 | |||||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Authors | Gong D / Dai X / Jih J / Liu YT / Bi GQ / Sun R / Zhou ZH | |||||||||||||||||||||||||||||||||||||||||||||
Funding support | United States, China, 14 items
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Citation | Journal: Cell / Year: 2019 Title: DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV. Authors: Danyang Gong / Xinghong Dai / Jonathan Jih / Yun-Tao Liu / Guo-Qiang Bi / Ren Sun / Z Hong Zhou / Abstract: Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes ...Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV's dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development. | |||||||||||||||||||||||||||||||||||||||||||||
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_20431.map.gz | 193.1 MB | EMDB map data format | |
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Header (meta data) | emd-20431-v30.xml emd-20431.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20431_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_20431.png | 284.8 KB | ||
Others | emd_20431_half_map_1.map.gz emd_20431_half_map_2.map.gz | 170.4 MB 170.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20431 | HTTPS FTP |
-Validation report
Summary document | emd_20431_validation.pdf.gz | 79.6 KB | Display | EMDB validaton report |
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Full document | emd_20431_full_validation.pdf.gz | 78.6 KB | Display | |
Data in XML | emd_20431_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20431 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20431 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20431.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: None
File | emd_20431_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_20431_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human gammaherpesvirus 8
Entire | Name: Human gammaherpesvirus 8 |
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Components |
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-Supramolecule #1: Human gammaherpesvirus 8
Supramolecule | Name: Human gammaherpesvirus 8 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 37296 / Sci species name: Human gammaherpesvirus 8 / Sci species strain: BAC16 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16 |
-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 temperature: 298 K / Instrument: HOMEMADE PLUNGER Details: The sample was manually blotted and frozen with a homemade plunger.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Max: 79.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 1440 pixel / Digitization - Dimensions - Height: 1440 pixel / Digitization - Sampling interval: 2.5 µm / Number real images: 8007 / Average exposure time: 13.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 24271 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 14000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |