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- EMDB-32106: The cryo-EM density map of the block of IBDV Gx strain -

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Basic information

Entry
Database: EMDB / ID: EMD-32106
TitleThe cryo-EM density map of the block of IBDV Gx strain
Map dataThe cryo-EM density map of the block of IBDV Gx strain
Sample
  • Virus: Infectious bursal disease virus (Gumboro virus)
Biological speciesInfectious bursal disease virus (Gumboro virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBao KY / Zhu P
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31430087 China
National Natural Science Foundation of China (NSFC)31425007 China
CitationJournal: Sci Bull (Beijing) / Year: 2022
Title: Cryo-EM structures of infectious bursal disease viruses with different virulences provide insights into their assembly and invasion
Authors: Bao K / Qi X / Lia Y / Gong M / Wang M / Zhu P
History
DepositionOct 25, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32106.png

Downloads & links

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Map

FileDownload / File: emd_32106.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM density map of the block of IBDV Gx strain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.19311164 - 0.31144863
Average (Standard dev.)0.0016248939 (±0.017544486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Infectious bursal disease virus

EntireName: Infectious bursal disease virus (Gumboro virus)
Components
  • Virus: Infectious bursal disease virus (Gumboro virus)

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Supramolecule #1: Infectious bursal disease virus

SupramoleculeName: Infectious bursal disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Gallus gallus (chicken)

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121881
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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