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- EMDB-8825: Cucumber necrosis virus, wild type, pH 5.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-8825
TitleCucumber necrosis virus, wild type, pH 5.0
Map dataWild type cucumber necrosis virus at pH 5.0
Sample
  • Virus: Cucumber necrosis virus
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesCucumber necrosis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsSmith TJ
CitationJournal: J Virol / Year: 2017
Title: Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission.
Authors: Michael B Sherman / Kishore Kakani / D'Ann Rochon / Wen Jiang / Neil R Voss / Thomas J Smith /
Abstract: (CNV) is a member of the genus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus As with other members of the genus, the CNV capsid swells ... (CNV) is a member of the genus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus As with other members of the genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). P73 lies immediately adjacent to a putative zinc binding site (M. Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) that is formed by three icosahedrally related His residues in the N termini of the C subunit at the quasi-6-fold axes. To better understand how this buried residue might affect vector transmission, we determined the cryo-electron microscopy structure of wild-type CNV in the native and swollen state and of the transmission-defective mutant, P73G, under native conditions. With the wild-type CNV, the swollen structure demonstrated the expected expansion of the capsid. However, the zinc binding region at the quasi-6-fold at the β-annulus axes remained intact. By comparison, the zinc binding region of the P73G mutant, even under native conditions, was markedly disordered, suggesting that the β-annulus had been disrupted and that this could destabilize the capsid. This was confirmed with pH and urea denaturation experiments in conjunction with electron microscopy analysis. We suggest that the P73G mutation affects the zinc binding and/or the β-annulus, making it more fragile under neutral/basic pH conditions. This, in turn, may affect zoospore transmission. (CNV), a member of the genus , is transmitted in nature via zoospores of the fungus While a number of plant viruses are transmitted via insect vectors, little is known at the molecular level as to how the viruses are recognized and transmitted. As with many spherical plant viruses, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation that lies inside the capsid immediately adjacent to a putative zinc binding site (Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). Here, we show that the P73G mutant is less stable than the wild type, and this appears to be correlated with destabilization of the β-annulus at the icosahedral 3-fold axes. Therefore, the β-annulus appears not to be essential for particle assembly but is necessary for interactions with the transmission vector.
History
DepositionJul 10, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateSep 27, 2017-
Current statusSep 27, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8825.png

Downloads & links

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Map

FileDownload / File: emd_8825.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWild type cucumber necrosis virus at pH 5.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 480 pix.
= 633.6 Å		1.32 Å/pix.
x 480 pix.
= 633.6 Å		1.32 Å/pix.
x 480 pix.
= 633.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 5
Minimum - Maximum-0.3265092 - 14.896599
Average (Standard dev.)-0.0000031254367 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 633.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z633.600633.600633.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-240-240-240
NC/NR/NS480480480
D min/max/mean-0.32714.897-0.000

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Supplemental data

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Sample components

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Entire : Cucumber necrosis virus

EntireName: Cucumber necrosis virus
Components
  • Virus: Cucumber necrosis virus

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Supramolecule #1: Cucumber necrosis virus

SupramoleculeName: Cucumber necrosis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12143 / Sci species name: Cucumber necrosis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: OTHER / Average electron dose: 12.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 37970
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

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