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- EMDB-1512: CryoEM structure of Blackcurrant Reversion Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-1512
TitleCryoEM structure of Blackcurrant Reversion Virus
Map dataThis is a reconstruction of blackcurrant reversion virus at 17 angstrom resolution.
Sample
  • Sample: Purified blackcurrant reversion virus in 0.05 M Na-citrate buffer (pH 7.0)
  • Virus: Blackcurrant reversion virus
KeywordsCryo / electron / microscopy / structure / blackcurrant / reversion / virus
Biological speciesBlackcurrant reversion virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 17.0 Å
AuthorsSeitsonen JJT / Susi P / Lemmetty A / Butcher SJ
CitationJournal: Virology / Year: 2008
Title: Structure of the mite-transmitted Blackcurrant reversion nepovirus using electron cryo-microscopy.
Authors: Jani J T Seitsonen / Petri Susi / Anne Lemmetty / Sarah J Butcher /
Abstract: Blackcurrant reversion nepovirus (BRV; genus Nepovirus) has a single-stranded, bipartite RNA genome surrounded by 60 copies of a single capsid protein (CP). BRV is the most important mite-transmitted ...Blackcurrant reversion nepovirus (BRV; genus Nepovirus) has a single-stranded, bipartite RNA genome surrounded by 60 copies of a single capsid protein (CP). BRV is the most important mite-transmitted viral pathogen of the Ribes species. It is the causal agent of blackcurrant reversion disease. We determined the structure of BRV to 1.7 nm resolution using electron cryo- microscopy (cryoEM) and image reconstruction. The reconstruction reveals a pseudo T=3 viral capsid similar to that of tobacco ringspot virus (TRSV). We modelled the BRV capsid protein to that of TRSV and fitted it into the cryoEM reconstruction. The fit indicated that the extended C-terminus of BRV-CP is located on the capsid surface and the N-terminus on the interior. We generated peptide antibodies to two putatively exposed C-terminal sequences and these reacted with the virus. Hence homology modelling may be useful for defining epitopes for antibody generation for diagnostic testing of BRV in commercial crops.
History
DepositionJun 3, 2008-
Header (metadata) releaseJun 3, 2008-
Map releaseMar 31, 2009-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2541.092691638
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2541.092691638
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1512.gif

Downloads & links

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Map

FileDownload / File: emd_1512.map.gz / Format: CCP4 / Size: 30.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a reconstruction of blackcurrant reversion virus at 17 angstrom resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 201 pix.
= 201.32 Å		2.26 Å/pix.
x 201 pix.
= 201.32 Å		2.26 Å/pix.
x 201 pix.
= 201.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.26203 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2480.0 / Movie #1: 2541.0926916
Minimum - Maximum0.0 - 4100.979999999999563
Average (Standard dev.)304.451000000000022 (±815.909999999999968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions201201201
Spacing201201201
CellA=B=C: 201.32 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.26202247191012.26202247191012.2620224719101
M x/y/z898989
origin x/y/z0.0000.0000.000
length x/y/z201.320201.320201.320
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS201201201
D min/max/mean0.0004100.983304.451

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Supplemental data

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Sample components

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Entire : Purified blackcurrant reversion virus in 0.05 M Na-citrate buffer...

EntireName: Purified blackcurrant reversion virus in 0.05 M Na-citrate buffer (pH 7.0)
Components
  • Sample: Purified blackcurrant reversion virus in 0.05 M Na-citrate buffer (pH 7.0)
  • Virus: Blackcurrant reversion virus

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Supramolecule #1000: Purified blackcurrant reversion virus in 0.05 M Na-citrate buffer...

SupramoleculeName: Purified blackcurrant reversion virus in 0.05 M Na-citrate buffer (pH 7.0)
type: sample / ID: 1000
Details: The sample was stored at -80 degrees celcius and thawed before loading onto grids
Oligomeric state: Complete particle, (60-mer) with the RNA genome inside
Number unique components: 1
Molecular weightExperimental: 3.30 MDa / Theoretical: 3.45 MDa
Method: SDS-PAGE (55 kDa per capsid protein, 60 capsid proteins per capsid) (Lemmetty et al. 1997, The American Phytopathology Society)

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Supramolecule #1: Blackcurrant reversion virus

SupramoleculeName: Blackcurrant reversion virus / type: virus / ID: 1 / Name.synonym: BRV / NCBI-ID: 65743 / Sci species name: Blackcurrant reversion virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: BRV
Host (natural)Organism: Chenopodium quinoa (quinoa) / synonym: PLANTAE(HIGHER PLANTS)
Molecular weightExperimental: 3.30 MDa / Theoretical: 3.45 MDa
Virus shellShell ID: 1 / Name: Coat protein / Diameter: 290 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

Concentration1 mg/mL
BufferpH: 7 / Details: 0.05 M Na-citrate buffer
StainingType: NEGATIVE
Details: Vitrified. Grids were blotted for roughly one second before being plunged into liquid ethane.
GridDetails: C-Flat 224 grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Guillotine / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 66400 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.6 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 68000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: astigmatism was corrected at 62000x magnification
DetailsPart of the data was recorded on Kodak SO163 film at nominal magnification of 50000.
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 65 / Average electron dose: 17 e/Å2
Details: 65 images total, 10 images were scanned from film using Zeiss Photoscan TD scanner with a stepsize of 7 micrometers.
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT, POR, EM3DR, P3DR
Details: Particles from CCD data and film data were combined for the final reconstruction.
Number images used: 831

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