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- EMDB-46991: Kaposi's sarcoma-associated herpesvirus (KSHV) penton vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-46991
TitleKaposi's sarcoma-associated herpesvirus (KSHV) penton vertex
Map data
Sample
  • Virus: Human gammaherpesvirus 8
KeywordsKaposi's sarcoma-associated herpesvirus / herpesvirus / KSHV / capsid / HHV-8 / penton / vertex / VIRUS
Biological speciesHuman gammaherpesvirus 8
Methodsubtomogram averaging / cryo EM / Resolution: 7.4 Å
AuthorsZhen J / Zhou ZH
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01 DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI175798 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01 DE027901 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32 AI060567 United States
American Cancer SocietyIRG-15-173-21 United States
CitationJournal: bioRxiv / Year: 2024
Title: Structures of Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus virions reveal species-specific tegument and envelope features.
Authors: James Zhen / Jia Chen / Haigen Huang / Shiqing Liao / Shiheng Liu / Yan Yuan / Ren Sun / Richard Longnecker / Ting-Ting Wu / Z Hong Zhou
Abstract: Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) are classified into the gammaherpesvirus subfamily of , which stands out from its alpha- and betaherpesvirus relatives due ...Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) are classified into the gammaherpesvirus subfamily of , which stands out from its alpha- and betaherpesvirus relatives due to the tumorigenicity of its members. Although structures of human alpha- and betaherpesviruses by cryogenic electron tomography (cryoET) have been reported, reconstructions of intact human gammaherpesvirus virions remain elusive. Here, we structurally characterize extracellular virions of EBV and KSHV by deep learning-enhanced cryoET, resolving both previously known monomorphic capsid structures and previously unknown pleomorphic features beyond the capsid. Through subtomogram averaging and subsequent tomogram-guided sub-particle reconstruction, we determined the orientation of KSHV nucleocapsids from mature virions with respect to the portal to provide spatial context for the tegument within the virion. Both EBV and KSHV have an eccentric capsid position and polarized distribution of tegument. Tegument species span from the capsid to the envelope and may serve as scaffolds for tegumentation and envelopment. The envelopes of EBV and KSHV are less densely populated with glycoproteins than those of herpes simplex virus 1 and human cytomegalovirus, representative members of alpha- and betaherpesviruses, respectively. This population density of glycoproteins correlates with their relative infectivity against HEK293T cells. Also, we observed fusion protein gB trimers exist within triplet arrangements in addition to standalone complexes, which is relevant to understanding dynamic processes such as fusion pore formation. Taken together, this study reveals nuanced yet important differences in the tegument and envelope architectures among human herpesviruses and provides insights into their varied cell tropism and infection.
IMPORTANCE: Discovered in 1964, Epstein-Barr virus (EBV) is the first identified human oncogenic virus and the founding member of the gammaherpesvirus subfamily. In 1994, another cancer-causing virus ...IMPORTANCE: Discovered in 1964, Epstein-Barr virus (EBV) is the first identified human oncogenic virus and the founding member of the gammaherpesvirus subfamily. In 1994, another cancer-causing virus was discovered in lesions of AIDS patients and later named Kaposi's sarcoma-associated herpesvirus (KSHV), the second human gammaherpesvirus. Despite the historical importance of EBV and KSHV, technical difficulties with isolating large quantities of these viruses and the pleiomorphic nature of their envelope and tegument layers have limited structural characterization of their virions. In this study, we employed the latest technologies in cryogenic electron microscopy (cryoEM) and tomography (cryoET) supplemented with an artificial intelligence-powered data processing software package to reconstruct 3D structures of the EBV and KSHV virions. We uncovered unique properties of the envelope glycoproteins and tegument layers of both EBV and KSHV. Comparison of these features with their non-tumorigenic counterparts provides insights into their relevance during infection.
History
DepositionSep 11, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46991.png

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Map

FileDownload / File: emd_46991.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 192 pix.
= 529.92 Å		2.76 Å/pix.
x 192 pix.
= 529.92 Å		2.76 Å/pix.
x 192 pix.
= 529.92 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
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Contour LevelBy AUTHOR: 0.00596
Minimum - Maximum-0.018411757 - 0.031879194
Average (Standard dev.)0.00074680435 (±0.0021716962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 529.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46991_msk_1.map
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Half map: #1

Fileemd_46991_half_map_1.map
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Half map: #2

Fileemd_46991_half_map_2.map
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Sample components

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Entire : Human gammaherpesvirus 8

EntireName: Human gammaherpesvirus 8
Components
  • Virus: Human gammaherpesvirus 8

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Supramolecule #1: Human gammaherpesvirus 8

SupramoleculeName: 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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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 3815
ExtractionNumber tomograms: 199 / Number images used: 7200 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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