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- EMDB-34235: Cryo-EM structure of Singapore Grouper Iridovirus capsid block 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-34235
TitleCryo-EM structure of Singapore Grouper Iridovirus capsid block 3
Map data
Sample
  • Virus: Singapore grouper iridovirus
Biological speciesSingapore grouper iridovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsZhao ZN / Liu CC / Zhu DJ / Qi JX / Zhang XZ / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly.
Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang ...Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang / Qiwei Qin / George F Gao /
Abstract: Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and ...Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and significantly threatens global biodiversity. In recent years, high morbidity and mortality in aquatic animals have been caused by iridovirid infections worldwide. Effective control and prevention strategies are urgently needed. Here, we present a near-atomic architecture of the SGIV capsid and identify eight types of capsid proteins. The viral inner membrane-integrated anchor protein colocalizes with the endoplasmic reticulum (ER), supporting the hypothesis that the biogenesis of the inner membrane is associated with the ER. Additionally, immunofluorescence assays indicate minor capsid proteins (mCPs) could form various building blocks with major capsid proteins (MCPs) before the formation of a viral factory (VF). These results expand our understanding of the capsid assembly of NCVs and provide more targets for vaccine and drug design to fight iridovirid infections.
History
DepositionSep 6, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_34235.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.04439521 - 0.09780498
Average (Standard dev.)0.00036216577 (±0.0037534365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34235_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_34235_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Sample components

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Entire : Singapore grouper iridovirus

EntireName: Singapore grouper iridovirus
Components
  • Virus: Singapore grouper iridovirus

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Supramolecule #1: Singapore grouper iridovirus

SupramoleculeName: Singapore grouper iridovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#14 / NCBI-ID: 262968 / Sci species name: Singapore grouper iridovirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1917620

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