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- EMDB-6403: Infectious bursal disease virus polyprotein and large precursors ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6403
TitleInfectious bursal disease virus polyprotein and large precursors assemble into a procapsid that is matured by its embedded protease
Map dataReconstruction of IBDV VLP
Sample
  • Sample: IBDV VLP
  • Virus: Infectious bursal disease virus (Gumboro virus)
Keywordscryo-electron microscopy / IBDV / procapsid / viral protease / protein processing / protein self-assembly / virus assembly / virus structure
Biological speciesInfectious bursal disease virus (Gumboro virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsCastrillo-Briceno M / Gomez-Blanco J / Monton M / Rueda P / Caston JR
CitationJournal: To Be Published
Title: Infectious bursal disease virus polyprotein and large precursors assemble into a procapsid that is matured by its embedded protease
Authors: Castrillo-Briceno M / Gomez-Blanco J / Monton M / Rueda P / Caston JR
History
DepositionJul 31, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseAug 3, 2016-
UpdateFeb 8, 2017-
Current statusFeb 8, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6403.gif

Downloads & links

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Map

FileDownload / File: emd_6403.map.gz / Format: CCP4 / Size: 35 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of IBDV VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.21 Å/pix.
x 211 pix.
= 888.31 Å		4.21 Å/pix.
x 211 pix.
= 888.31 Å		4.21 Å/pix.
x 211 pix.
= 888.31 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.02795656 - 0.05186027
Average (Standard dev.)0.00084067 (±0.00767857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions211211211
Spacing211211211
CellA=B=C: 888.31 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.214.214.21
M x/y/z211211211
origin x/y/z0.0000.0000.000
length x/y/z888.310888.310888.310
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS211211211
D min/max/mean-0.0280.0520.001

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Supplemental data

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Sample components

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Entire : IBDV VLP

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

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Supramolecule #1000: IBDV VLP

SupramoleculeName: IBDV VLP / type: sample / ID: 1000 / Oligomeric state: 60 copies arranged into 20 trimers / Number unique components: 1
Molecular weightTheoretical: 2.8 MDa

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Supramolecule #1: Infectious bursal disease virus

SupramoleculeName: Infectious bursal disease virus / type: virus / ID: 1 / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Sci species strain: Soroa / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Gallus gallus (chicken) / synonym: VERTEBRATES
Host systemOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: H5
Molecular weightTheoretical: 2.8 MDa
Virus shellShell ID: 1 / Diameter: 700 Å / T number (triangulation number): 13

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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: 6.2 / Details: 150 mM NaCl, 20 mM CaCl2
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TECNAI F20
DateMay 1, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 424

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