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- PDB-9vjd: Cucumber Green Mottle Mosaic Virus (CGMMV) coat protein -

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Basic information

Entry
Database: PDB / ID: 9vjd
TitleCucumber Green Mottle Mosaic Virus (CGMMV) coat protein
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Helical / RNA virus / Coat protein subunit / VIRUS
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesCucumber green mottle mosaic virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsChatterjee, A. / Venkatasubramanian, A. / Jailani, A.K. / Das, U. / Ragunath, V.K. / Mandal, B. / Datta, P.P.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentSTARS/APR2019/BS/581/FS India
CitationJournal: To Be Published
Title: Cucumber Green Mottle Mosaic Virus (CGMMV) coat protein
Authors: Chatterjee, A. / Venkatasubramanian, A. / Jailani, A.K. / Das, U. / Ragunath, V.K. / Mandal, B. / Datta, P.P.
History
DepositionJun 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)16,7881
Polymers16,7881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Capsid protein / Coat protein


Mass: 16787.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumber green mottle mosaic virus (strain watermelon SH)
Strain: watermelon SH / Gene: CP / Production host: Lagenaria siceraria (white-flowered gourd) / References: UniProt: P69474
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Cucumber green mottle mosaic virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Cucumber green mottle mosaic virus
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Lagenaria siceraria
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35.82 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1.0particle selection
4CTFFIND4.1CTF correction
7Coot0.9.8.95model fitting
12cryoSPARC4.3.03D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 22 ° / Axial rise/subunit: 1.4 Å / Axial symmetry: C1
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2038 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
RefinementHighest resolution: 2.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0041211
ELECTRON MICROSCOPYf_angle_d0.6361653
ELECTRON MICROSCOPYf_dihedral_angle_d3.688168
ELECTRON MICROSCOPYf_chiral_restr0.042194
ELECTRON MICROSCOPYf_plane_restr0.004217

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