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- EMDB-30248: CryoEM structure of VZV A-capsid, 3-fold sub-particle reconstruction -

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Entry
Database: EMDB / ID: EMD-30248
TitleCryoEM structure of VZV A-capsid, 3-fold sub-particle reconstruction
Map dataCryoEM structure of VZV A-capsid (3-fold sub-particle reconstruction)
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi S / Zheng Q
CitationJournal: Nat Microbiol / Year: 2020
Title: Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids.
Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que ...Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que / Ting Wu / Jun Zhang / Shaowei Li / Hua Zhu / Z Hong Zhou / Tong Cheng / Ningshao Xia /
Abstract: Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo- ...Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome that is substantially smaller than those of other human herpesviruses, VZV has a similarly sized capsid, consisting of 955 major capsid protein (MCP), 900 small capsid protein (SCP), 640 triplex dimer (Tri2) and 320 triplex monomer (Tri1) subunits. The VZV capsid has high thermal stability, although with relatively fewer intra- and inter-capsid protein interactions and less stably associated tegument proteins compared with other human herpesviruses. Analysis with antibodies targeting the N and C termini of the VZV SCP indicates that the hexon-capping SCP-the largest among human herpesviruses-uses its N-terminal half to bridge hexon MCP subunits and possesses a C-terminal flexible half emanating from the inner rim of the upper hexon channel into the tegument layer. Correlation of these structural features and functional observations provide insights into VZV assembly and pathogenesis and should help efforts to engineer gene delivery and anticancer vectors based on the currently available VZV vaccine.
History
DepositionApr 26, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 11, 2021-
Current statusAug 11, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 9.44
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30248.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of VZV A-capsid (3-fold sub-particle reconstruction)
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 9.44 / Movie #1: 9.44
Minimum - Maximum-29.575521 - 47.775623
Average (Standard dev.)0.014513213 (±3.4053464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 705.78 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z705.780705.780705.780
α/β/γ90.00090.00090.000
start NX/NY/NZ594743
NX/NY/NZ375263
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS540540540
D min/max/mean-29.57647.7760.015

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Supplemental data

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Sample components

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Entire : Human alphaherpesvirus 3

EntireName: Human alphaherpesvirus 3 (Varicella-zoster virus)
Components
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)

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Supramolecule #1: Human alphaherpesvirus 3

SupramoleculeName: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / 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
VitrificationCryogen name: 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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 459660

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