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- EMDB-5536: Visualization of Bacteriophage T7 Infection by Cryo-Electron Tomo... -

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Basic information

Entry
Database: EMDB / ID: EMD-5536
TitleVisualization of Bacteriophage T7 Infection by Cryo-Electron Tomography
Map dataAsymmetric reconstruction of bacteriophage fiberless virion
Sample
  • Sample: Bacteriophage T7 fiberless virion
  • Virus: Enterobacteria phage T7 (virus)
KeywordsBacteriophage infection E. coli minicell DNA ejection
Biological speciesEnterobacteria phage T7 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsHu B / Margolin W / Molineux IJ / Liu J
CitationJournal: Science / Year: 2013
Title: The bacteriophage t7 virion undergoes extensive structural remodeling during infection.
Authors: Bo Hu / William Margolin / Ian J Molineux / Jun Liu /
Abstract: Adsorption and genome ejection are fundamental to the bacteriophage life cycle, yet their molecular mechanisms are not well understood. We used cryo-electron tomography to capture T7 virions at ...Adsorption and genome ejection are fundamental to the bacteriophage life cycle, yet their molecular mechanisms are not well understood. We used cryo-electron tomography to capture T7 virions at successive stages of infection of Escherichia coli minicells at ~4-nm resolution. The six phage tail fibers were folded against the capsid, extending and orienting symmetrically only after productive adsorption to the host cell surface. Receptor binding by the tail triggered conformational changes resulting in the insertion of an extended tail, which functions as the DNA ejection conduit into the cell cytoplasm. After ejection, the extended phage tail collapsed or disassembled, which allowed resealing of the infected cell membrane. These structural studies provide a detailed series of intermediates during phage infection.
History
DepositionDec 4, 2012-
Header (metadata) releaseJul 3, 2013-
Map releaseSep 4, 2013-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5536.jpg

Downloads & links

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Map

FileDownload / File: emd_5536.map.gz / Format: CCP4 / Size: 13.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of bacteriophage fiberless virion
Voxel sizeX=Y=Z: 5.7 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.09669447 - 4.93614149
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-90
Dimensions140140180
Spacing140140180
CellA: 798.0 Å / B: 798.0 Å / C: 1026.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.75.75.7
M x/y/z140140180
origin x/y/z0.0000.0000.000
length x/y/z798.000798.0001026.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-70-70-90
NC/NR/NS140140180
D min/max/mean-4.0974.9360.000

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Supplemental data

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Sample components

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Entire : Bacteriophage T7 fiberless virion

EntireName: Bacteriophage T7 fiberless virion
Components
  • Sample: Bacteriophage T7 fiberless virion
  • Virus: Enterobacteria phage T7 (virus)

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Supramolecule #1000: Bacteriophage T7 fiberless virion

SupramoleculeName: Bacteriophage T7 fiberless virion / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage T7

SupramoleculeName: Enterobacteria phage T7 / type: virus / ID: 1 / Name.synonym: Bacteriophage T7 mutant / NCBI-ID: 10760 / Sci species name: Enterobacteria phage T7 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Bacteriophage T7 mutant
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid / Diameter: 600 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8 / Details: 50 mM Tris-HCl, 10 mM MgCl2, 0.1 M NaCl
GridDetails: 200 mesh grid
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 31000
Sample stageSpecimen holder: Liquid Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
TemperatureMin: 90 K / Max: 100 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000x magnification
DateJul 17, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 100 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: No CTF correction
Final 3D classificationNumber classes: 4
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Raptor, Protomo / Number subtomograms used: 1945
DetailsThe particles were manually selected from cryo-tomograms.

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