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- EMDB-3131: Visualizing the Adsorption of Cyanophage P-SSP7 to the Marine Cya... -

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Basic information

Entry
Database: EMDB / ID: EMD-3131
TitleVisualizing the Adsorption of Cyanophage P-SSP7 to the Marine Cyanobacterium Prochlorococcus MED4 by Electron Cryo-Tomography
Map datapre-infection conformation of P-SSP7 bacteriophage
Sample
  • Sample: Pre-infection comformation of Prochlorococcus phage P-SSP7
  • Virus: Prochlorococcus phage P-SSP7 (virus)
Keywordscryo-electron tomography / bacteriophage / cyanobacteria
Biological speciesProchlorococcus phage P-SSP7 (virus)
Methodsubtomogram averaging / cryo EM
AuthorsMurata K / Zhang Q / Fu C / Liu X / Sullivan M / Coleman M / Osburne M / Schmid MF / Chisholm S / Chiu W
CitationJournal: Sci Rep / Year: 2017
Title: Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus.
Authors: Kazuyoshi Murata / Qinfen Zhang / Jesús Gerardo Galaz-Montoya / Caroline Fu / Maureen L Coleman / Marcia S Osburne / Michael F Schmid / Matthew B Sullivan / Sallie W Chisholm / Wah Chiu /
Abstract: Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium ...Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococcus MED4 and its associated cyanophage P-SSP7 have revealed complex gene expression dynamics once infection has begun, but the initial cyanophage-host interactions remain poorly understood. Here, we used single particle cryo-electron tomography (cryo-ET) to investigate cyanophage-host interactions in this model system, based on 170 cyanophage-to-host adsorption events. Subtomogram classification and averaging revealed three main conformations characterized by different angles between the phage tail and the cell surface. Namely, phage tails were (i) parallel to, (ii) ~45 degrees to, or (iii) perpendicular to the cell surface. Furthermore, different conformations of phage tail fibers correlated with the aforementioned orientations of the tails. We also observed density beyond the tail tip in vertically-oriented phages that had penetrated the cell wall, capturing the final stage of adsorption. Together, our data provide a quantitative characterization of the orientation of phages as they adsorb onto cells, and suggest that cyanophages that abut their cellular targets are only transiently in the "perpendicular" orientation required for successful infection.
History
DepositionAug 16, 2015-
Header (metadata) releaseSep 16, 2015-
Map releaseFeb 1, 2017-
UpdateFeb 1, 2017-
Current statusFeb 1, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3131.jpg

Downloads & links

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Map

FileDownload / File: emd_3131.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpre-infection conformation of P-SSP7 bacteriophage
Voxel sizeX=Y=Z: 9.36 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-9.39850712 - 17.140092849999998
Average (Standard dev.)0.00171619 (±0.99989992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 1684.7999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.369.369.36
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z1684.8001684.8001684.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-9.39917.1400.002

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Supplemental data

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Sample components

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Entire : Pre-infection comformation of Prochlorococcus phage P-SSP7

EntireName: Pre-infection comformation of Prochlorococcus phage P-SSP7
Components
  • Sample: Pre-infection comformation of Prochlorococcus phage P-SSP7
  • Virus: Prochlorococcus phage P-SSP7 (virus)

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Supramolecule #1000: Pre-infection comformation of Prochlorococcus phage P-SSP7

SupramoleculeName: Pre-infection comformation of Prochlorococcus phage P-SSP7
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Prochlorococcus phage P-SSP7

SupramoleculeName: Prochlorococcus phage P-SSP7 / type: virus / ID: 1 / NCBI-ID: 268748 / Sci species name: Prochlorococcus phage P-SSP7 / Sci species strain: P-SSP7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Prochlorococcus (bacteria) / Strain: MED4 / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 655 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
Details: 100 mM Tris-HCl (pH 7.5), 100 mM MgSO4, and 30 mM NaCl
GridDetails: R3.5/1 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 120 K / Instrument: LEICA EM CPC
Method: Grids with sample solution were quickly frozen in liquid ethane.

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 20000
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 62 °
TemperatureAverage: 90 K
DateMay 16, 2008
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 80 e/Å2 / Bits/pixel: 16

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution method: OTHER / Software - Name: EMAN1 / Number subtomograms used: 44

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