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- EMDB-6402: Infectious bursal disease virus polyprotein and large precursors ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6402
TitleInfectious bursal disease virus polyprotein and large precursors assemble into a procapsid that is matured by its embedded protease
Map dataReconstruction of IBDV procapsid
Sample
  • Sample: IBDV procapsid
  • 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: 25.0 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: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6402.png

Downloads & links

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Map

FileDownload / File: emd_6402.map.gz / Format: CCP4 / Size: 86.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of IBDV procapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.51 Å/pix.
x 285 pix.
= 1570.35 Å		5.51 Å/pix.
x 285 pix.
= 1570.35 Å		5.51 Å/pix.
x 285 pix.
= 1570.35 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.5.515.515.51
CCP4 map header5.515.515.51
EM Navigator Movie #12.7552.7552.755
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.02398811 - 0.03207992
Average (Standard dev.)0.00165585 (±0.00638837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions285285285
Spacing285285285
CellA=B=C: 1570.3501 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.515.515.51
M x/y/z285285285
origin x/y/z0.0000.0000.000
length x/y/z1570.3501570.3501570.350
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS285285285
D min/max/mean-0.0240.0320.002

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Supplemental data

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Sample components

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Entire : IBDV procapsid

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

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Supramolecule #1000: IBDV procapsid

SupramoleculeName: IBDV procapsid / 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: No
Host (natural)Organism: Gallus gallus (chicken) / synonym: VERTEBRATES
Host systemOrganism: Coturnix japonica (Japanese quail) / Recombinant cell: QM7
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 GP

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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: 25.0 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 369

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