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- EMDB-1237: Infectious bursal disease virus capsid assembly and maturation by... -

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Basic information

Entry
Database: EMDB / ID: EMD-1237
TitleInfectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch.
Map dataDensity map of the T=1 Infectious Bursal Disease Virus (IBDV) Subviral Particle (SVP)2X2Y2Z oriented.
Sample
  • Sample: Infectious Bursal Disease Virus Subviral Particle
  • Virus: Infectious bursal disease virus (Gumboro virus)
Biological speciesInfectious bursal disease virus (Gumboro virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.2 Å
AuthorsLuque D / Saugar I / Rodriguez JF / Verdaguer N / Garriga D / San Martin C / Velazquez-Muriel JA / Trus BL / Carrascosa JL / Caston JR
CitationJournal: J Virol / Year: 2007
Title: Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch.
Authors: Daniel Luque / Irene Saugar / José F Rodríguez / Nuria Verdaguer / Damiá Garriga / Carmen San Martín / Javier A Velázquez-Muriel / Benes L Trus / José L Carrascosa / José R Castón /
Abstract: Infectious bursal disease virus (IBDV), a double-stranded RNA (dsRNA) virus belonging to the Birnaviridae family, is an economically important avian pathogen. The IBDV capsid is based on a single- ...Infectious bursal disease virus (IBDV), a double-stranded RNA (dsRNA) virus belonging to the Birnaviridae family, is an economically important avian pathogen. The IBDV capsid is based on a single-shelled T=13 lattice, and the only structural subunits are VP2 trimers. During capsid assembly, VP2 is synthesized as a protein precursor, called pVP2, whose 71-residue C-terminal end is proteolytically processed. The conformational flexibility of pVP2 is due to an amphipathic alpha-helix located at its C-terminal end. VP3, the other IBDV major structural protein that accomplishes numerous roles during the viral cycle, acts as a scaffolding protein required for assembly control. Here we address the molecular mechanism that defines the multimeric state of the capsid protein as hexamers or pentamers. We used a combination of three-dimensional cryo-electron microscopy maps at or close to subnanometer resolution with atomic models. Our studies suggest that the key polypeptide element, the C-terminal amphipathic alpha-helix, which acts as a transient conformational switch, is bound to the flexible VP2 C-terminal end. In addition, capsid protein oligomerization is also controlled by the progressive trimming of its C-terminal domain. The coordination of these molecular events correlates viral capsid assembly with different conformations of the amphipathic alpha-helix in the precursor capsid, as a five-alpha-helix bundle at the pentamers or an open star-like conformation at the hexamers. These results, reminiscent of the assembly pathway of positive single-stranded RNA viruses, such as nodavirus and tetravirus, add new insights into the evolutionary relationships of dsRNA viruses.
History
DepositionJul 10, 2006-
Header (metadata) releaseJul 10, 2006-
Map releaseMay 2, 2007-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1237.gif

Downloads & links

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Map

FileDownload / File: emd_1237.map.gz / Format: CCP4 / Size: 53.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of the T=1 Infectious Bursal Disease Virus (IBDV) Subviral Particle (SVP)2X2Y2Z oriented.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 243 pix.
= 340.2 Å		1.4 Å/pix.
x 243 pix.
= 340.2 Å		1.4 Å/pix.
x 243 pix.
= 340.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.338 / Movie #1: 0.4
Minimum - Maximum-2.20102 - 3.09582
Average (Standard dev.)0.00422405 (±0.263223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-121-121-121
Dimensions243243243
Spacing243243243
CellA=B=C: 340.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z243243243
origin x/y/z0.0000.0000.000
length x/y/z340.200340.200340.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-121-121-121
NC/NR/NS243243243
D min/max/mean-2.2013.0960.004

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Supplemental data

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Sample components

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Entire : Infectious Bursal Disease Virus Subviral Particle

EntireName: Infectious Bursal Disease Virus Subviral Particle
Components
  • Sample: Infectious Bursal Disease Virus Subviral Particle
  • Virus: Infectious bursal disease virus (Gumboro virus)

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Supramolecule #1000: Infectious Bursal Disease Virus Subviral Particle

SupramoleculeName: Infectious Bursal Disease Virus Subviral Particle / type: sample / ID: 1000 / Oligomeric state: 60 copies of VP2 arranged in 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 / Name.synonym: Gumboro virus, subviral particle / Details: IBDV Capsid Protein / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Gumboro virus, subviral particle
Host (natural)Organism: Gallus gallus (chicken) / synonym: VERTEBRATES
Molecular weightExperimental: 2.880 MDa
Virus shellShell ID: 1 / Name: IBDV Subviral particle / Diameter: 260 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.2 / Details: 25 mM PIPES, 150 mM NaCl, and 20 mM CaCl2
StainingType: NEGATIVE
Details: Samples containing were applied to one side of a holey carbon film, washed twice on water drops, blotted, and plunged into a liquid ethane bath following standard procedures
GridDetails: 300 mesh holey carbon film
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 23 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: em3dr2
Details: Resolution for SVP was also evaluated by FSC calculated between the full-dataset map and the SVP atomic map and for a correlation limit of 0.3, this was at 6.6 A.
Number images used: 23754

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Atomic model buiding 1

Initial modelPDB ID:

1wcd

SoftwareName: SITUS and URO
DetailsProtocol: Rigid body. Refinement was done in both Real and Fourier Sapce
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC and R-factor

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Atomic model buiding 2

Initial modelPDB ID:

2gsy

SoftwareName: SITUS and URO
DetailsProtocol: Rigid body. Refinement was done in both Real and Fourier Sapce
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC and R-factor

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