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- EMDB-6468: Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM... -

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Basic information

Entry
Database: EMDB / ID: EMD-6468
TitleUncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis
Map dataCa-pH7
Sample
  • Sample: Carnation mottle virus
  • Virus: Carnation mottle virus
Biological speciesCarnation mottle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsWang CY / Zhang QF / Gao YZ / Xie L / Li HM / Hong J / Zhang CX
CitationJournal: Sci Rep / Year: 2015
Title: Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis.
Authors: Chun-Yan Wang / Qin-Fen Zhang / Yuan-Zhu Gao / Li Xie / Hong-Mei Li / Jian Hong / Chuan-Xi Zhang /
Abstract: Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we ...Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we obtained two reconstructions of CarMV at pH7 in the presence (Ca-pH7) and absence (EDTA-pH7) of calcium ions by Cryo-EM single particle analysis, which achieved 6.4 Å and 8 Å resolutions respectively. Our results showed that chelation of the calcium ions under EDTA-pH7 resulted in reduced interaction between the subunits near the center of the asymmetric unit but not overall size change of the viral particles, which indicated that the role of the calcium ions in CarMV was not predominantly for the structural preservation. Part of the genomic RNA closest to the capsid was found to be located near the center of the asymmetric unit, which might result from the interaction between genomic RNA and Lys194 residues. Together with the electrostatic potential analysis on the inner surface of the asymmetric unit, the reduced interaction near the center of the asymmetric unit under EDTA-pH7 suggested that the genome release of CarMV might be realized through the center of the asymmetric unit.
History
DepositionSep 17, 2015-
Header (metadata) releaseNov 4, 2015-
Map releaseSep 21, 2016-
UpdateSep 21, 2016-
Current statusSep 21, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6468.map.gz / Format: CCP4 / Size: 268.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCa-pH7
Voxel sizeX=Y=Z: 1.192 Å
Density
Contour LevelBy EMDB: 1.06 / Movie #1: 2.5
Minimum - Maximum-6.63813591 - 11.09692287
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208-208-208
Dimensions416416416
Spacing416416416
CellA=B=C: 495.872 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1921.1921.192
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z495.872495.872495.872
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-208-208-208
NC/NR/NS416416416
D min/max/mean-6.63811.097-0.000

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Supplemental data

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Sample components

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Entire : Carnation mottle virus

EntireName: Carnation mottle virus
Components
  • Sample: Carnation mottle virus
  • Virus: Carnation mottle virus

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Supramolecule #1000: Carnation mottle virus

SupramoleculeName: Carnation mottle virus / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Carnation mottle virus

SupramoleculeName: Carnation mottle virus / type: virus / ID: 1 / NCBI-ID: 11986 / Sci species name: Carnation mottle virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Dianthus caryophyllus (clove pink) / synonym: PLANTAE(HIGHER PLANTS)

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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

VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateOct 11, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: OTHER / Number images used: 8400

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Atomic model buiding 1

Initial modelPDB ID:
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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