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- EMDB-60696: Cucumber Green Mottle Mosaic Virus (CGMMV)coat protein assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-60696
TitleCucumber Green Mottle Mosaic Virus (CGMMV)coat protein assembly
Map dataThe map shows the helical arrangement of coat protein subunits of CGMMV. The RNA density, embedded inside the coat protein assembly, can be seen in higher contour level.
Sample
  • Virus: Cucumber green mottle mosaic virus
    • Other: Cucumber Green Mottle Mosaic Virus
KeywordsHelical / RNA virus / VIRUS
Biological speciesCucumber green mottle mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsChatterjee A / Venkatasubramanian A / Jailani AK / Das U / Ragunath VK / Mandal B / Datta PP
Funding support1 items
OrganizationGrant numberCountry
Other governmentSTARS/APR2019/BS/581/FS
CitationJournal: To Be Published
Title: Cucumber Green Mottle Mosaic Virus (CGMMV)coat protein assembly
Authors: Chatterjee A / Venkatasubramanian A / Jailani AK / Das U / Ragunath VK / Mandal B / Datta PP
History
DepositionJul 4, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60696.png

Downloads & links

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Map

FileDownload / File: emd_60696.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map shows the helical arrangement of coat protein subunits of CGMMV. The RNA density, embedded inside the coat protein assembly, can be seen in higher contour level.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.97
Minimum - Maximum-1.9445976 - 6.667731
Average (Standard dev.)0.08791406 (±0.46268395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60696_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_60696_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_60696_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cucumber green mottle mosaic virus

EntireName: Cucumber green mottle mosaic virus
Components
  • Virus: Cucumber green mottle mosaic virus
    • Other: Cucumber Green Mottle Mosaic Virus

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Supramolecule #1: Cucumber green mottle mosaic virus

SupramoleculeName: Cucumber green mottle mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12235 / Sci species name: Cucumber green mottle mosaic virus / Sci species strain: Bg / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Lagenaria siceraria (white-flowered gourd)

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Macromolecule #1: Cucumber Green Mottle Mosaic Virus

MacromoleculeName: Cucumber Green Mottle Mosaic Virus / type: other / ID: 1 / Classification: other
Source (natural)Organism: Cucumber green mottle mosaic virus
SequenceString:
MAYNPITPSK LIAFSASYVP VRTLLNFLVA SQGTAFQTQA GRDSFRESLS ALPSSVVDIN SRFPDAGFYA FLNGPVLRPI FVSLLSSTDT RNRVIEVVDP SNPTTAESLN AVKRTDDAST AARAEIDNLI ESISKGFDVY DRASFEAAFS VVWSEATTSK A

GENBANK: GENBANK: DQ767631.2

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 35.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 22 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.0) / Number images used: 2038
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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