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- EMDB-8869: Bacteriophage Sf14 Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-8869
TitleBacteriophage Sf14 Capsid
Map dataIcosahedrally averaged map of capsid of phage Sf14.
Sample
  • Virus: Bacteriophage Sf14 (virus)
Biological speciesBacteriophage Sf14 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.2 Å
AuthorsDoore SM / Schrad JR / Dean WF / Dover JA / Parent KN
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM110185 United States
National Science Foundation (NSF, United States)DBI-0939454 United States
CitationJournal: J Virol / Year: 2018
Title: Shigella Phages Isolated during a Dysentery Outbreak Reveal Uncommon Structures and Broad Species Diversity.
Authors: Sarah M Doore / Jason R Schrad / William F Dean / John A Dover / Kristin N Parent /
Abstract: In 2016, Michigan experienced the largest outbreak of shigellosis, a type of bacillary dysentery caused by spp., since 1988. Following this outbreak, we isolated 16 novel -infecting bacteriophages ...In 2016, Michigan experienced the largest outbreak of shigellosis, a type of bacillary dysentery caused by spp., since 1988. Following this outbreak, we isolated 16 novel -infecting bacteriophages (viruses that infect bacteria) from environmental water sources. Most well-known bacteriophages infect the common laboratory species and , and these phages have built the foundation of molecular and bacteriophage biology. Until now, comparatively few bacteriophages were known to infect spp., which are close relatives of We present a comprehensive analysis of these phages' host ranges, genomes, and structures, revealing genome sizes and capsid properties that are shared by very few previously described phages. After sequencing, a majority of the phages were found to have genomes of an uncommon size, shared by only 2% of all reported phage genomes. To investigate the structural implications of this unusual genome size, we used cryo-electron microscopy to resolve their capsid structures. We determined that these bacteriophage capsids have similarly uncommon geometry. Only two other viruses with this capsid structure have been described. Since most well-known bacteriophages infect or , our understanding of bacteriophages has been limited to a subset of well-described systems. Continuing to isolate phages using nontraditional strains of bacteria can fill gaps that currently exist in bacteriophage biology. In addition, the prevalence of phages during a shigellosis outbreak may suggest a potential impact of human health epidemics on local microbial communities. spp. bacteria are causative agents of dysentery and affect more than 164 million people worldwide every year. Despite the need to combat antibiotic-resistant strains, relatively few -infecting bacteriophages have been described. By specifically looking for -infecting phages, this work has identified new isolates that (i) may be useful to combat infections and (ii) fill gaps in our knowledge of bacteriophage biology. The rare qualities of these new isolates emphasize the importance of isolating phages on "nontraditional" laboratory strains of bacteria to more fully understand both the basic biology and diversity of bacteriophages.
History
DepositionAug 1, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 171
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 171
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8869.png

Downloads & links

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Map

FileDownload / File: emd_8869.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedrally averaged map of capsid of phage Sf14.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.07 Å/pix.
x 679 pix.
= 1405.53 Å		2.07 Å/pix.
x 679 pix.
= 1405.53 Å		2.07 Å/pix.
x 679 pix.
= 1405.53 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 171 / Movie #1: 171
Minimum - Maximum-454.23587 - 642.6853
Average (Standard dev.)0.7753399 (±52.68091)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions679679679
Spacing679679679
CellA=B=C: 1405.5299 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.072.072.07
M x/y/z679679679
origin x/y/z0.0000.0000.000
length x/y/z1405.5301405.5301405.530
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS679679679
D min/max/mean-454.236642.6850.775

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Supplemental data

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Sample components

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Entire : Bacteriophage Sf14

EntireName: Bacteriophage Sf14 (virus)
Components
  • Virus: Bacteriophage Sf14 (virus)

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Supramolecule #1: Bacteriophage Sf14

SupramoleculeName: Bacteriophage Sf14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 38018 / Sci species name: Bacteriophage Sf14 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri (bacteria) / Strain: PE577
Virus shellShell ID: 1 / Name: Capsid / Diameter: 786.0 Å / T number (triangulation number): 9

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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: 7.6
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
10.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details1.8 x 10^12 phage/mL

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureMin: 83.0 K / Max: 83.0 K
Specialist opticsEnergy filter - Name: JEOL Omega / Energy filter - Lower energy threshold: 35 eV / Energy filter - Upper energy threshold: 35 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4866 pixel / Digitization - Dimensions - Height: 3411 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 44 / Average exposure time: 1.0 sec. / Average electron dose: 10.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.9 µm / Calibrated defocus min: 0.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 278
CTF correctionSoftware - Name: Auto3DEM (ver. 4.05.1)
Startup modelType of model: OTHER / Details: Random Model Computation
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3DEM (ver. 4.05.1) / Number images used: 276
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: Auto3DEM (ver. 4.05.1)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 60
Projection matching processing - Angular sampling: 1.0 degrees
Software - Name: Auto3DEM (ver. 4.05.1)
Details: Iterative procedure starting at 1 degree sampling, ending at 0.4 degrees imposing icosahedral symmetry.

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