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- EMDB-31609: Cryo-EM structure of PRV C-capsid 2-fold sub-particle -

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Basic information

Entry
Database: EMDB / ID: EMD-31609
TitleCryo-EM structure of PRV C-capsid 2-fold sub-particle
Map data
Sample
  • Virus: Suid alphaherpesvirus 1
Biological speciesSuid alphaherpesvirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsZheng Q / Li S / Zha Z / Sun H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structures of pseudorabies virus capsids.
Authors: Guosong Wang / Zhenghui Zha / Pengfei Huang / Hui Sun / Yang Huang / Maozhou He / Tian Chen / Lina Lin / Zhenqin Chen / Zhibo Kong / Yuqiong Que / Tingting Li / Ying Gu / Hai Yu / Jun Zhang ...Authors: Guosong Wang / Zhenghui Zha / Pengfei Huang / Hui Sun / Yang Huang / Maozhou He / Tian Chen / Lina Lin / Zhenqin Chen / Zhibo Kong / Yuqiong Que / Tingting Li / Ying Gu / Hai Yu / Jun Zhang / Qingbing Zheng / Yixin Chen / Shaowei Li / Ningshao Xia /
Abstract: Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral ...Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral encephalitis caused by PRV infection, suggesting that PRV may be able to overcome the species barrier to infect humans. To date, there is no available therapeutic for PRV infection. Here, we report the near-atomic structures of the PRV A-capsid and C-capsid, and illustrate the interaction that occurs between these subunits. We show that the C-capsid portal complex is decorated with capsid-associated tegument complexes. The PRV capsid structure is highly reminiscent of other α-herpesviruses, with some additional structural features of β- and γ-herpesviruses. These results illustrate the structure of the PRV capsid and elucidate the underlying assembly mechanism at the molecular level. This knowledge may be useful for the development of oncolytic agents or specific therapeutics against this arm of the herpesvirus family.
History
DepositionAug 2, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31609.png

Downloads & links

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Map

FileDownload / File: emd_31609.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 480 pix.
= 536.16 Å		1.12 Å/pix.
x 480 pix.
= 536.16 Å		1.12 Å/pix.
x 480 pix.
= 536.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.117 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-10.592722 - 16.810366
Average (Standard dev.)0.006225382 (±1.6591496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 536.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Suid alphaherpesvirus 1

EntireName: Suid alphaherpesvirus 1
Components
  • Virus: Suid alphaherpesvirus 1

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Supramolecule #1: Suid alphaherpesvirus 1

SupramoleculeName: Suid alphaherpesvirus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10345 / Sci species name: Suid alphaherpesvirus 1 / 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 TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 427560
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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