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- EMDB-3509: IBDV E1-1B population -

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Basic information

Entry
Database: EMDB / ID: EMD-3509
TitleIBDV E1-1B population
Map data
Sample
  • Virus: Infectious bursal disease virus (Gumboro virus)
Biological speciesInfectious bursal disease virus (Gumboro virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.6 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: 0.002
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3509.png

Downloads & links

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Map

FileDownload / File: emd_3509.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.32 Å
Density
Contour LevelBy EMDB: 0.01 / Movie #1: 0.002
Minimum - Maximum-0.02663855 - 0.043779865
Average (Standard dev.)0.0008595971 (±0.0067509133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 864.00006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.324.324.32
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z864.000864.000864.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0270.0440.001

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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
Processingsingle particle reconstruction
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 F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 5.0 µm / Calibrated defocus min: 0.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 10.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5565
Details: Includes E1-1A and E1-1B particles further classified
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

1118

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 2 / Avg.num./class: 2027 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 20.6 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 2027

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