|Entry||Database: EMDB / ID: EMD-20437|
|Title||Kaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodecamer structure|
|Sample||Human gammaherpesvirus 8:|
virus / Portal protein
|Function / homology||Herpesvirus portal protein / DNA packaging / viral release from host cell / virion / host cell nucleus / Portal protein / Portal protein|
Function and homology information
|Biological species||Human gammaherpesvirus 8 / HHV-8 (virus)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.7 Å|
|Authors||Gong D / Dai X / Jih J / Liu YT / Bi GQ / Sun R / Zhou ZH|
|Funding support|| United States, China, 14 items |
|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.
|Validation Report||PDB-ID: 6ppi|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_20437.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.03 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Human gammaherpesvirus 8
|Entire||Name: Human gammaherpesvirus 8 / Number of components: 2|
-Component #1: virus, Human gammaherpesvirus 8
|Virus||Name: Human gammaherpesvirus 8Kaposi's sarcoma-associated herpesvirus|
Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
|Species||Species: Human gammaherpesvirus 8 / Strain: BAC16|
|Source (natural)||Host Species: Homo sapiens (human)|
|Shell #1||Name of element: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16|
-Component #2: protein, Portal protein
|Protein||Name: Portal protein|
Details: Subunit of portal complex present at KSHV's portal vertex; 12 copies constitute one dodecameric complex
Number of Copies: 12 / Recombinant expression: No
|Mass||Theoretical: 68.087516 kDa|
|Source||Species: HHV-8 (virus) / Strain: GK18|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K|
Details: The sample was manually blotted and frozen with a homemade plunger..
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 14000.0 X (nominal), 24271.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: ( - 79.0 K)|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 8007 / Sampling size: 2.5 µm|
|Processing||Method: single particle reconstruction / Applied symmetry: C12 (12 fold cyclic) / Number of projections: 39073|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 200|
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