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- EMDB-2242: The Cryo-EM structure of Arabis mosaic virus -

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Basic information

Entry
Database: EMDB / ID: EMD-2242
TitleThe Cryo-EM structure of Arabis mosaic virus
Map data3D cryo-EM map of ArMV
Sample
  • Sample: Purified ArMV particle containing its RNA
  • Virus: Arabis mosaic virus
KeywordsArabis mosaic virus / Nepovirus / cryo-electron microscopy / image processing / molecular dynamics flexible fitting / nematode transmission
Biological speciesArabis mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsLai-Kee-Him J / Schellenberger P / Dumas C / Richard E / Trapani S / Komar V / Demangeat G / Ritzenthaler C / Bron P
CitationJournal: J Struct Biol / Year: 2013
Title: The backbone model of the Arabis mosaic virus reveals new insights into functional domains of Nepovirus capsid.
Authors: Joséphine Lai-Kee-Him / Pascale Schellenberger / Christian Dumas / Eric Richard / Stefano Trapani / Véronique Komar / Gerard Demangeat / Christophe Ritzenthaler / Patrick Bron /
Abstract: Arabis mosaic virus (ArMV) and Grapevine fanleaf virus (GFLV) are two picorna-like viruses from the genus Nepovirus, consisting in a bipartite RNA genome encapsidated into a 30 nm icosahedral viral ...Arabis mosaic virus (ArMV) and Grapevine fanleaf virus (GFLV) are two picorna-like viruses from the genus Nepovirus, consisting in a bipartite RNA genome encapsidated into a 30 nm icosahedral viral particle formed by 60 copies of a single capsid protein (CP). They are responsible for a severe degeneration of grapevines that occurs in most vineyards worldwide. Although sharing a high level of sequence identity between their CP, ArMV is transmitted exclusively by the ectoparasitic nematode Xiphinema diversicaudatum whereas GFLV is specifically transmitted by the nematode X. index. The structural determinants involved in the transmission specificity of both viruses map solely to their respective CP. Recently, reverse genetic and crystallographic studies on GFLV revealed that a positively charged pocket in the CP B domain located at the virus surface may be responsible for vector specificity. To go further into delineating the coat protein determinants involved in transmission specificity, we determined the 6.5 Å resolution cryo-electron microscopy structure of ArMV and used homology modeling and flexible fitting approaches to build its pseudo-atomic structure. This study allowed us to resolve ArMV CP architecture and delineate connections between ArMV capsid shell and its RNA. Comparison of ArMV and GFLV CPs reveals structural differences in the B domain pocket, thus strengthening the hypothesis of a key role of this region in the viral transmission specificity and identifies new potential functional domains of Nepovirus capsid.
History
DepositionDec 11, 2012-
Header (metadata) releaseJan 9, 2013-
Map releaseFeb 13, 2013-
UpdateMar 27, 2013-
Current statusMar 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 50.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2242.png

Downloads & links

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Map

FileDownload / File: emd_2242.map.gz / Format: CCP4 / Size: 82.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D cryo-EM map of ArMV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 281 pix.
= 418.69 Å		1.49 Å/pix.
x 281 pix.
= 418.69 Å		1.49 Å/pix.
x 281 pix.
= 418.69 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 50.299999999999997 / Movie #1: 50.3
Minimum - Maximum0.0 - 100.0
Average (Standard dev.)38.964431759999997 (±7.54202795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions281281281
Spacing281281281
CellA=B=C: 418.69 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.491.491.49
M x/y/z281281281
origin x/y/z0.0000.0000.000
length x/y/z418.690418.690418.690
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS281281281
D min/max/mean0.000100.00038.964

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Supplemental data

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Sample components

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Entire : Purified ArMV particle containing its RNA

EntireName: Purified ArMV particle containing its RNA
Components
  • Sample: Purified ArMV particle containing its RNA
  • Virus: Arabis mosaic virus

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Supramolecule #1000: Purified ArMV particle containing its RNA

SupramoleculeName: Purified ArMV particle containing its RNA / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Arabis mosaic virus

SupramoleculeName: Arabis mosaic virus / type: virus / ID: 1 / Name.synonym: ArMV
Details: The virion is purified from infected plants and contains its RNA
NCBI-ID: 12271 / Sci species name: Arabis mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: ArMV
Host (natural)Organism: Chenopodium quinoa (quinoa) / synonym: PLANTAE(HIGHER PLANTS)
Virus shellShell ID: 1 / Diameter: 300 Å / T number (triangulation number): 3

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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

Concentration2 mg/mL
BufferpH: 7
Details: 15 mM sodium phosphate and 5 mM potassium phosphate pH 7.0
GridDetails: Quantifoil R 2/2 grids (Quantifoil Micro Tools GmbH, Jena, Germany)
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 103.15 K / Instrument: GATAN CRYOPLUNGE 3
Method: blotted for 1s and then flash frozen in liquid ethane

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureAverage: 93.15 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Specialist opticsEnergy filter - Name: omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateSep 1, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 7 µm / Number real images: 400 / Average electron dose: 18 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 46980 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000
Sample stageSpecimen holder: gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsImage processing was performed using AUTO3DEM package
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: BOXER, CTFFIND3, CTFMIX, AUTO3DEM / Number images used: 7009

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