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- EMDB-3513: IBDV E3 population -

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Basic information

Entry
Database: EMDB / ID: EMD-3513
TitleIBDV E3 population
Map data
Sample
  • Virus: Infectious bursal disease virus (Gumboro virus)
Biological speciesInfectious bursal disease virus (Gumboro virus)
Methodsubtomogram averaging / cryo EM / Resolution: 53.3 Å
AuthorsMata CP / Mertens J / Fontana J / Luque D / Allende-Ballestero C / Reguera D / Trus BL / Steven AC / Carrascosa JL / Caston JR
CitationJournal: J Virol / Year: 2018
Title: The RNA-Binding Protein of a Double-Stranded RNA Virus Acts like a Scaffold Protein.
Authors: Carlos P Mata / Johann Mertens / Juan Fontana / Daniel Luque / Carolina Allende-Ballestero / David Reguera / Benes L Trus / Alasdair C Steven / José L Carrascosa / José R Castón /
Abstract: Infectious bursal disease virus (IBDV), a nonenveloped, double-stranded RNA (dsRNA) virus with a T=13 icosahedral capsid, has a virion assembly strategy that initiates with a precursor particle based ...Infectious bursal disease virus (IBDV), a nonenveloped, double-stranded RNA (dsRNA) virus with a T=13 icosahedral capsid, has a virion assembly strategy that initiates with a precursor particle based on an internal scaffold shell similar to that of tailed double-stranded DNA (dsDNA) viruses. In IBDV-infected cells, the assembly pathway results mainly in mature virions that package four dsRNA segments, although minor viral populations ranging from zero to three dsRNA segments also form. We used cryo-electron microscopy (cryo-EM), cryo-electron tomography, and atomic force microscopy to characterize these IBDV populations. The VP3 protein was found to act as a scaffold protein by building an irregular, ∼40-Å-thick internal shell without icosahedral symmetry, which facilitates formation of a precursor particle, the procapsid. Analysis of IBDV procapsid mechanical properties indicated a VP3 layer beneath the icosahedral shell, which increased the effective capsid thickness. Whereas scaffolding proteins are discharged in tailed dsDNA viruses, VP3 is a multifunctional protein. In mature virions, VP3 is bound to the dsRNA genome, which is organized as ribonucleoprotein complexes. IBDV is an amalgam of dsRNA viral ancestors and traits from dsDNA and single-stranded RNA (ssRNA) viruses. Structural analyses highlight the constraint of virus evolution to a limited number of capsid protein folds and assembly strategies that result in a functional virion. We report the cryo-EM and cryo-electron tomography structures and the results of atomic force microscopy studies of the infectious bursal disease virus (IBDV), a double-stranded RNA virus with an icosahedral capsid. We found evidence of a new inner shell that might act as an internal scaffold during IBDV assembly. The use of an internal scaffold is reminiscent of tailed dsDNA viruses, which constitute the most successful self-replicating system on Earth. The IBDV scaffold protein is multifunctional and, after capsid maturation, is genome bound to form ribonucleoprotein complexes. IBDV encompasses numerous functional and structural characteristics of RNA and DNA viruses; we suggest that IBDV is a modern descendant of ancestral viruses and comprises different features of current viral lineages.
History
DepositionNov 24, 2016-
Header (metadata) releaseDec 28, 2016-
Map releaseAug 22, 2018-
UpdateMar 6, 2019-
Current statusMar 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3513.png

Downloads & links

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Map

FileDownload / File: emd_3513.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.6 Å/pix.
x 148 pix.
= 828.8 Å		5.6 Å/pix.
x 148 pix.
= 828.8 Å		5.6 Å/pix.
x 148 pix.
= 828.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.4170002 - 0.5405388
Average (Standard dev.)0.0000028742968 (±0.14334014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions148148148
Spacing148148148
CellA=B=C: 828.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.65.65.6
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z828.800828.800828.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS148148148
D min/max/mean-0.4170.5410.000

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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 / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Gallus gallus (chicken)
Molecular weightExperimental: 50 MDa
Virus shellShell ID: 1 / Name: VP2 / Diameter: 700.0 Å / T number (triangulation number): 13

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6.2 / Details: 25 mM PIPES pH 6.2, 150 mM NaCl, 20 mM CaCl2
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TECNAI 12
Specialist opticsEnergy filter - Name: GIF 2002 Gatan
Image recordingFilm or detector model: OTHER / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated defocus max: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 53600
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 53.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp (ver. 2) / Number subtomograms used: 95
ExtractionNumber tomograms: 3 / Number images used: 95 / Software - Name: Bsoft (ver. 1.9)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp (ver. 2)

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