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- EMDB-35600: Cryo-Em structure of the middle part of the shrimp white spot syn... -

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Basic information

Entry
Database: EMDB / ID: EMD-35600
TitleCryo-Em structure of the middle part of the shrimp white spot syndrome virus nucleocapsid (narrow type)
Map data
Sample
  • Virus: White spot syndrome virus
Biological speciesWhite spot syndrome virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsHuang HJ / Wang HC
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 108-2314-B-006-096-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 108-2112-M-002-016-MY3 Taiwan
CitationJournal: Int J Mol Sci / Year: 2023
Title: Multiple Nucleocapsid Structural Forms of Shrimp White Spot Syndrome Virus Suggests a Novel Viral Morphogenetic Pathway.
Authors: Hui-Ju Huang / Sen-Lin Tang / Yuan-Chih Chang / Hao-Ching Wang / Tze Hann Ng / Rees F Garmann / Yu-Wen Chen / Jiun-Yan Huang / Ramya Kumar / Sheng-Hsiung Chang / Shang-Rung Wu / Chih-Yu Chao ...Authors: Hui-Ju Huang / Sen-Lin Tang / Yuan-Chih Chang / Hao-Ching Wang / Tze Hann Ng / Rees F Garmann / Yu-Wen Chen / Jiun-Yan Huang / Ramya Kumar / Sheng-Hsiung Chang / Shang-Rung Wu / Chih-Yu Chao / Kyoko Matoba / Iwasaki Kenji / William M Gelbart / Tzu-Ping Ko / Hwei-Jiung Andrew Wang / Chu-Fang Lo / Li-Li Chen / Han-Ching Wang /
Abstract: White spot syndrome virus (WSSV) is a very large dsDNA virus. The accepted shape of the WSSV virion has been as ellipsoidal, with a tail-like extension. However, due to the scarcity of reliable ...White spot syndrome virus (WSSV) is a very large dsDNA virus. The accepted shape of the WSSV virion has been as ellipsoidal, with a tail-like extension. However, due to the scarcity of reliable references, the pathogenesis and morphogenesis of WSSV are not well understood. Here, we used transmission electron microscopy (TEM) and cryogenic electron microscopy (Cryo-EM) to address some knowledge gaps. We concluded that mature WSSV virions with a stout oval-like shape do not have tail-like extensions. Furthermore, there were two distinct ends in WSSV nucleocapsids: a portal cap and a closed base. A C14 symmetric structure of the WSSV nucleocapsid was also proposed, according to our Cryo-EM map. Immunoelectron microscopy (IEM) revealed that VP664 proteins, the main components of the 14 assembly units, form a ring-like architecture. Moreover, WSSV nucleocapsids were also observed to undergo unique helical dissociation. Based on these new results, we propose a novel morphogenetic pathway of WSSV.
History
DepositionMar 10, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35600.png

Downloads & links

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Map

FileDownload / File: emd_35600.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.048552893 - 0.054671425
Average (Standard dev.)0.00029685433 (±0.0024467057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 1059.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_35600_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35600_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35600_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : White spot syndrome virus

EntireName: White spot syndrome virus
Components
  • Virus: White spot syndrome virus

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Supramolecule #1: White spot syndrome virus

SupramoleculeName: White spot syndrome virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 342409 / Sci species name: White spot syndrome virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Shrimp white spot syndrome virus / Strain: AF440570

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 274 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 73000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15279

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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