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- EMDB-41213: Human cytomegalovirus portal vertex-resolved capsid, virion confi... -

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Basic information

Entry
Database: EMDB / ID: EMD-41213
TitleHuman cytomegalovirus portal vertex-resolved capsid, virion configuration 1 (VC1)
Map dataPrimary map.
Sample
  • Virus: Human herpesvirus 5 strain AD169
Keywordstegument / portal / capsid / intracellular transport / VIRUS
Biological speciesHuman herpesvirus 5 strain AD169
Methodsingle particle reconstruction / cryo EM / Resolution: 10.88 Å
AuthorsJih J / Liu YT / Liu W / Zhou H
Funding support United States, 9 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)T32AR071307 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P30 AI152501 United States
James B. Pendleton Charitable Trust (to the UCLA AIDS Institute) United States
McCarthy Family Foundation (to the UCLA AIDS Institute) United States
National Institutes of Health/Office of the Director1S10RR23057 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Sci Adv / Year: 2024
Title: The incredible bulk: Human cytomegalovirus tegument architectures uncovered by AI-empowered cryo-EM.
Authors: Jonathan Jih / Yun-Tao Liu / Wei Liu / Z Hong Zhou /
Abstract: The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between ...The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning-enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head-linker-capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.
History
DepositionJul 7, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41213.png

Downloads & links

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Map

FileDownload / File: emd_41213.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map.
Voxel sizeX=Y=Z: 5.44 Å
Density
Contour LevelBy AUTHOR: 0.0162
Minimum - Maximum-0.024968203 - 0.062760144
Average (Standard dev.)0.0034047074 (±0.008693735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 1740.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Post-processed map for visualization.

Fileemd_41213_additional_1.map
AnnotationPost-processed map for visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_41213_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_41213_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human herpesvirus 5 strain AD169

EntireName: Human herpesvirus 5 strain AD169
Components
  • Virus: Human herpesvirus 5 strain AD169

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Supramolecule #1: Human herpesvirus 5 strain AD169

SupramoleculeName: Human herpesvirus 5 strain AD169 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 / NCBI-ID: 10360 / Sci species name: Human herpesvirus 5 strain AD169 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Virion capsid / T number (triangulation number): 16

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 47.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 367007
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30047
FSC plot (resolution estimation)

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