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- EMDB-33163: 3D structure of the base in oval-shaped WSSV capsids -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33163
Title3D structure of the base in oval-shaped WSSV capsids
Map data
Sample
  • Complex: wssv
KeywordsComplex / C14 / capsid / base / VIRAL PROTEIN
Biological speciesWhite spot syndrome virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 5.88 Å
AuthorsShan H / Liu MD / Shen QT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870743 China
CitationJournal: To Be Published
Title: 3D structure of the base in oval-shaped WSSV capsids
Authors: Shan H / Liu MD / Shen QT
History
DepositionMar 31, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33163.png

Downloads & links

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Map

FileDownload / File: emd_33163.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.01 Å/pix.
x 400 pix.
= 804. Å		2.01 Å/pix.
x 400 pix.
= 804. Å		2.01 Å/pix.
x 400 pix.
= 804. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.766
Minimum - Maximum-0.5568403 - 1.8872045
Average (Standard dev.)0.04937146 (±0.17145127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 804.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33163_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_33163_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 : wssv

EntireName: wssv
Components
  • Complex: wssv

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Supramolecule #1: wssv

SupramoleculeName: wssv / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: White spot syndrome virus

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: uranyl acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1683
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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