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- EMDB-9676: Vibrio phage M4 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-9676
TitleVibrio phage M4 capsid
Map dataThe icosahedral capsid of an El Tor vibriophage M4.
Sample
  • Virus: Viruses
Biological speciesViruses
Methodsingle particle reconstruction / cryo EM / Resolution: 15.4 Å
AuthorsDas S / Dutta M / Sen A / Ghosh AN
Funding support India, 1 items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research21(0948)/13/EMR-II India
CitationJournal: Arch Virol / Year: 2019
Title: Structural analysis and proteomics studies on the Myoviridae vibriophage M4.
Authors: Sayani Das / Moumita Dutta / Anindito Sen / Amar N Ghosh /
Abstract: Bacteriophages play a crucial role in tracking the spread of bacterial epidemics. The frequent emergence of antibiotic-resistant bacterial strains throughout the world has motivated studies on ...Bacteriophages play a crucial role in tracking the spread of bacterial epidemics. The frequent emergence of antibiotic-resistant bacterial strains throughout the world has motivated studies on bacteriophages that can potentially be used in phage therapy as an alternative to conventional antibiotic treatment. A recent outbreak of cholera in Haiti took many lives due to a rapid development of resistance to the available antibiotics. The properties of vibriophages, bacteriophages that infect Vibrio cholerae, are therefore of practical interest. A detailed understanding of the structure and assembly of a vibriophage is potentially useful in developing phage therapy against cholera as well as for fabricating artificial nanocontainers. Therefore, the aim of the present study was to determine the three-dimensional organization of vibriophage M4 at sub-nanometer resolution by electron microscopy and single-particle analysis techniques to facilitate its use as a therapeutic agent. We found that M4 has a large capsid with T = 13 icosahedral symmetry and a long contractile tail. This double-stranded DNA phage also contains a head-to-tail connector protein complex that joins the capsid to the tail and a prominent baseplate at the end of the tail. This study also provides information regarding the proteome of this phage, which is proteins similar to that of other Myoviridae phages, and most of the encoded proteins are structural proteins that form the exquisite architecture of this bacteriophage.
History
DepositionOct 8, 2018-
Header (metadata) releaseOct 9, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.17
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9676.png

Downloads & links

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Map

FileDownload / File: emd_9676.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe icosahedral capsid of an El Tor vibriophage M4.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.59 Å/pix.
x 360 pix.
= 933.048 Å		2.59 Å/pix.
x 360 pix.
= 933.048 Å		2.59 Å/pix.
x 360 pix.
= 933.048 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5918 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.17 / Movie #1: 1.17
Minimum - Maximum-0.1417114 - 5.0684667
Average (Standard dev.)0.15158607 (±0.4668119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 933.048 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.59182.59182.5918
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z933.048933.048933.048
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ224224224
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.1425.0680.152

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Supplemental data

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Sample components

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Entire : Viruses

EntireName: Viruses
Components
  • Virus: Viruses

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Supramolecule #1: Viruses

SupramoleculeName: Viruses / type: virus / ID: 1 / Parent: 0 / Details: Vibrio phage M4, ATCC number-51354-B4 / NCBI-ID: 10239 / Sci species name: Viruses / Sci species strain: M4 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vibrio cholerae MAK 757 (bacteria)
Virus shellShell ID: 1 / Name: Vibrio phage M4 capsid / Diameter: 800.0 Å / T number (triangulation number): 13

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 500
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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