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- EMDB-6382: Three-dimensional structure of Maize Chlorotic Mottle Virus by Si... -

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Basic information

Entry
Database: EMDB / ID: EMD-6382
TitleThree-dimensional structure of Maize Chlorotic Mottle Virus by Single Particle Analysis
Map dataReconstruction of Maize Chlorotic Mottle Virus by Single Particle Analysis
Sample
  • Sample: Maize Chloroltic Mottle Virus
  • Virus: Maize chlorotic mottle 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 / Capsid protein
Function and homology information
Biological speciesMaize chlorotic mottle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang CY / Zhang QF / Gao YZ / Zhou XP / Ji G / Huang XJ / Hong J / Zhang CY
CitationJournal: Virology / Year: 2015
Title: Insight into the three-dimensional structure of maize chlorotic mottle virus revealed by Cryo-EM single particle analysis.
Authors: Chun-Yan Wang / Qin-Fen Zhang / Yuan-Zhu Gao / Xue-Ping Zhou / Gang Ji / Xiao-Jun Huang / Jian Hong / Chuan-Xi Zhang /
Abstract: Maize chlorotic mottle virus (MCMV) is the only member of the Machlomovirus genus in the family Tombusviridae. Here, we obtained the Cryo-EM structure of MCMV by single particle analysis with most ...Maize chlorotic mottle virus (MCMV) is the only member of the Machlomovirus genus in the family Tombusviridae. Here, we obtained the Cryo-EM structure of MCMV by single particle analysis with most local resolution at approximately 4 Å. The Cα backbone was built based on residues with bulky side chains. The resolved C-terminus of the capsid protein subunit and obvious openings at the 2-fold axis demonstrated the compactness of the asymmetric unit, which indicates an important role in the stability of MCMV. The Asp116 residue from each subunit around the 5-fold and 3-fold axes contributed to the negative charges in the centers of the pentamers and hexamers, which might serve as a solid barrier against the leakage of genomic RNA. Finally, the loops most exposed on the surface were analyzed and are proposed to be potential functional sites related to MCMV transmission.
History
DepositionJul 10, 2015-
Header (metadata) releaseOct 21, 2015-
Map releaseJul 13, 2016-
UpdateJul 13, 2016-
Current statusJul 13, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6382.tif

emd_6382_1.tif

Downloads & links

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Map

FileDownload / File: emd_6382.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Maize Chlorotic Mottle Virus by Single Particle Analysis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 300 pix.
= 358.8 Å		1.2 Å/pix.
x 300 pix.
= 358.8 Å		1.2 Å/pix.
x 300 pix.
= 358.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.196 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.0 / Movie #1: 2
Minimum - Maximum-6.67525434 - 12.20485687
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 358.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1961.1961.196
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z358.800358.800358.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-6.67512.205-0.000

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Supplemental data

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Sample components

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Entire : Maize Chloroltic Mottle Virus

EntireName: Maize Chloroltic Mottle Virus
Components
  • Sample: Maize Chloroltic Mottle Virus
  • Virus: Maize chlorotic mottle virus

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Supramolecule #1000: Maize Chloroltic Mottle Virus

SupramoleculeName: Maize Chloroltic Mottle Virus / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Maize chlorotic mottle virus

SupramoleculeName: Maize chlorotic mottle virus / type: virus / ID: 1 / NCBI-ID: 12138 / Sci species name: Maize chlorotic mottle virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Zea mays subsp. mays (maize) / synonym: PLANTAE(HIGHER PLANTS)
Virus shellShell ID: 1 / 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

VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateOct 20, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Number images used: 53600

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