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- EMDB-2063: A 3-D cryo-electron microscopy structure of bacteriophage phi92 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2063
TitleA 3-D cryo-electron microscopy structure of bacteriophage phi92 capsid
Map dataReconstruction ofbacteriophage phi92 capsid
Sample
  • Sample: Bacteriophage phi92
  • Virus: Staphylococcus phage 92 (virus)
KeywordsBacteriophage / phi92 / capsid / single particle / cryo-electron / reconstruction
Biological speciesStaphylococcus phage 92 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å
AuthorsBrowning C / Nazarov S / Bowman V / Leiman P
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 29, 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: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2063.png

Downloads & links

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Map

FileDownload / File: emd_2063.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction ofbacteriophage phi92 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.81 Å/pix.
x 384 pix.
= 1079.04 Å		2.81 Å/pix.
x 384 pix.
= 1079.04 Å		2.81 Å/pix.
x 384 pix.
= 1079.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-5.35246372 - 6.91830111
Average (Standard dev.)0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 1079.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.812.812.81
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z1079.0401079.0401079.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-5.3526.9180.000

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Supplemental data

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Sample components

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Entire : Bacteriophage phi92

EntireName: Bacteriophage phi92 (virus)
Components
  • Sample: Bacteriophage phi92
  • Virus: Staphylococcus phage 92 (virus)

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Supramolecule #1000: Bacteriophage phi92

SupramoleculeName: Bacteriophage phi92 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Staphylococcus phage 92

SupramoleculeName: Staphylococcus phage 92 / type: virus / ID: 1 / Name.synonym: bacteriophage phi92 / Details: Bacteriophage phi92 is a large lytic myovirus / NCBI-ID: 320849 / Sci species name: Staphylococcus phage 92 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage phi92
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / T number (triangulation number): 13

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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: 100 % / Chamber temperature: 113 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

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Image processing

DetailsThe icosahedral reconstruction the phi92 capsid was calculated from scratch. The initial model was constructed with a small subset of initial data. This model was then subjected to several rounds of refinement until convergence.
CTF correctionDetails: Each Micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 1137
Final two d classificationNumber classes: 10

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Atomic model buiding 1

Initial modelPDB ID:

1ohg

SoftwareName: Chimera
RefinementSpace: REAL

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