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- EMDB-20560: Atomic Structure of the Human Herpesvirus 6B Capsid and Capsid-As... -

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Basic information

Entry
Database: EMDB / ID: EMD-20560
TitleAtomic Structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes
Map data3-fold sub-particle reconstruction of HHV-6B
Sample
  • Virus: Human herpesvirus 6 strain Z29
Biological speciesHuman herpesvirus 6 strain Z29
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsZhang YB / Liu W / Li ZH / Kumar V / Alvarez-Cabrera AL / Leibovitch E / Cui YX / Mei Y / Bi GQ / Jacobson S / Zhou ZH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, DE025567 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: Nat Commun / Year: 2019
Title: Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes.
Authors: Yibo Zhang / Wei Liu / Zihang Li / Vinay Kumar / Ana L Alvarez-Cabrera / Emily C Leibovitch / Yanxiang Cui / Ye Mei / Guo-Qiang Bi / Steve Jacobson / Z Hong Zhou /
Abstract: Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B ...Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae.
History
DepositionAug 3, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseDec 11, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20560.png

Downloads & links

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Map

FileDownload / File: emd_20560.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3-fold sub-particle reconstruction of HHV-6B
Voxel sizeX=Y=Z: 1.085 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.06510922 - 0.12458778
Average (Standard dev.)0.0014823362 (±0.007062441)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 542.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z542.500542.500542.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0650.1250.001

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Supplemental data

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Sample components

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Entire : Human herpesvirus 6 strain Z29

EntireName: Human herpesvirus 6 strain Z29
Components
  • Virus: Human herpesvirus 6 strain Z29

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Supramolecule #1: Human herpesvirus 6 strain Z29

SupramoleculeName: Human herpesvirus 6 strain Z29 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 36351 / Sci species name: Human herpesvirus 6 strain Z29 / Sci species strain: Z29 / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS buffer, pH 7.4
GridMaterial: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: The grids were manually plunged into the Ethane..

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 23.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: 3D reconstruction of extracted 3-fold sub-particles
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128860

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