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- EMDB-2064: A 3-D cryo-electron structure of bacteriophage phi92 baseplate -

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Basic information

Entry
Database: EMDB / ID: EMD-2064
TitleA 3-D cryo-electron structure of bacteriophage phi92 baseplate
Map dataReconstruction of bacteriophage phi92 baseplate
Sample
  • Sample: Base plate-tail complex of bacteriophage phi92
  • Protein or peptide: Baseplate-tail complex
KeywordsBacteriophage / coliphage / phi92 / single particle / cryo-electron / baseplate
Biological speciesStaphylococcus phage 92 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 26.0 Å
AuthorsBrowning C / Nazarov S / Bowman VD / Leiman PG
CitationJournal: J Virol / Year: 2012
Title: A multivalent adsorption apparatus explains the broad host range of phage phi92: a comprehensive genomic and structural analysis.
Authors: David Schwarzer / Falk F R Buettner / Christopher Browning / Sergey Nazarov / Wolfgang Rabsch / Andrea Bethe / Astrid Oberbeck / Valorie D Bowman / Katharina Stummeyer / Martina Mühlenhoff ...Authors: David Schwarzer / Falk F R Buettner / Christopher Browning / Sergey Nazarov / Wolfgang Rabsch / Andrea Bethe / Astrid Oberbeck / Valorie D Bowman / Katharina Stummeyer / Martina Mühlenhoff / Petr G Leiman / Rita Gerardy-Schahn /
Abstract: Bacteriophage phi92 is a large, lytic myovirus isolated in 1983 from pathogenic Escherichia coli strains that carry a polysialic acid capsule. Here we report the genome organization of phi92, the ...Bacteriophage phi92 is a large, lytic myovirus isolated in 1983 from pathogenic Escherichia coli strains that carry a polysialic acid capsule. Here we report the genome organization of phi92, the cryoelectron microscopy reconstruction of its virion, and the reinvestigation of its host specificity. The genome consists of a linear, double-stranded 148,612-bp DNA sequence containing 248 potential open reading frames and 11 putative tRNA genes. Orthologs were found for 130 of the predicted proteins. Most of the virion proteins showed significant sequence similarities to proteins of myoviruses rv5 and PVP-SE1, indicating that phi92 is a new member of the novel genus of rv5-like phages. Reinvestigation of phi92 host specificity showed that the host range is not limited to polysialic acid-encapsulated Escherichia coli but includes most laboratory strains of Escherichia coli and many Salmonella strains. Structure analysis of the phi92 virion demonstrated the presence of four different types of tail fibers and/or tailspikes, which enable the phage to use attachment sites on encapsulated and nonencapsulated bacteria. With this report, we provide the first detailed description of a multivalent, multispecies phage armed with a host cell adsorption apparatus resembling a nanosized Swiss army knife. The genome, structure, and, in particular, the organization of the baseplate of phi92 demonstrate how a bacteriophage can evolve into a multi-pathogen-killing agent.
History
DepositionMar 30, 2012-
Header (metadata) releaseApr 5, 2012-
Map releaseJul 16, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0037
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0037
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2064.png

Downloads & links

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Map

FileDownload / File: emd_2064.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of bacteriophage phi92 baseplate
Voxel sizeX=Y=Z: 4.216 Å
Density
Contour LevelBy EMDB: 0.005 / Movie #1: 0.0037
Minimum - Maximum-0.01484859 - 0.02372414
Average (Standard dev.)0.00008039 (±0.00163187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 843.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.2164.2164.216
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z843.200843.200843.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0150.0240.000

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Supplemental data

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Sample components

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Entire : Base plate-tail complex of bacteriophage phi92

EntireName: Base plate-tail complex of bacteriophage phi92
Components
  • Sample: Base plate-tail complex of bacteriophage phi92
  • Protein or peptide: Baseplate-tail complex

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Supramolecule #1000: Base plate-tail complex of bacteriophage phi92

SupramoleculeName: Base plate-tail complex of bacteriophage phi92 / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Baseplate-tail complex

MacromoleculeName: Baseplate-tail complex / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Staphylococcus phage 92 (virus) / synonym: coliphage phi92

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferDetails: 50mM TrisCl pH 7.5, 100mM NaCl, 8mM MgSO4
StainingType: NEGATIVE / Details: vitrification in liquid ethane
GridDetails: holey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 113 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER
DateMay 30, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 38 / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: Each Micrograph
Final two d classificationNumber classes: 10
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, EMAN / Number images used: 985
DetailsThe reconstruction was performed by imposing 6-fold symmetry averaging. The 6-fold axis is along Z.

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