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- EMDB-9679: Tail structure of Vibrio phage M4 -

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Basic information

Entry
Database: EMDB / ID: EMD-9679
TitleTail structure of Vibrio phage M4
Map dataVibrio phage M4 contractile tail.
Sample
  • Virus: Viruses
Biological speciesViruses
Methodhelical reconstruction / negative staining / Resolution: 18.2 Å
AuthorsSen A / Das S / Dutta M / 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 10, 2018-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateOct 16, 2019-
Current statusOct 16, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 16.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 16.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9679.png

Downloads & links

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Map

FileDownload / File: emd_9679.map.gz / Format: CCP4 / Size: 6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVibrio phage M4 contractile tail.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 116 pix.
= 498.8 Å		4.3 Å/pix.
x 116 pix.
= 498.8 Å		4.3 Å/pix.
x 116 pix.
= 498.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 16.399999999999999 / Movie #1: 16.4
Minimum - Maximum-13.596428 - 34.204085999999997
Average (Standard dev.)1.8970867 (±6.5299454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-58-58-58
Dimensions116116116
Spacing116116116
CellA=B=C: 498.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z116116116
origin x/y/z0.0000.0000.000
length x/y/z498.800498.800498.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-58-58-58
NC/NR/NS116116116
D min/max/mean-13.59634.2041.897

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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 tail / Diameter: 240.0 Å

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 180.0 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
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 36.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 24.2 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 18.2 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 800
Final angle assignmentType: COMMON LINE

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