National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM071940
United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)
DE025567
United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)
DE028583
United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)
DE027901
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI094386
United States
National Institutes of Health/National Cancer Institute (NIH/NCI)
CA177322
United States
National Institutes of Health/National Cancer Institute (NIH/NCI)
CA091791
United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)
DE023591
United States
Other government
2017YFA0505300
China
Other government
2016YFA0400900
China
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
1S10RR23057
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
1U24GM116792
United States
National Science Foundation (NSF, United States)
DBI-1338135
United States
National Science Foundation (NSF, United States)
DMR-1548924
United States
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
Deposition
Jul 6, 2019
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Header (metadata) release
Jul 31, 2019
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Map release
Sep 11, 2019
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Update
Sep 6, 2023
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Current status
Sep 6, 2023
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER Details: The sample was manually blotted and frozen with a homemade plunger..
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Electron microscopy
Microscope
FEI TITAN KRIOS
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 1440 pixel / Digitization - Dimensions - Height: 1440 pixel / Number real images: 8007 / Average exposure time: 13.0 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 44328
Startup model
Type of model: NONE
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 39073
FSC plot (resolution estimation)
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