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- EMDB-5728: Icosahedrally-averaged bacteriophage Sf6 virion -

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Basic information

Entry
Database: EMDB / ID: EMD-5728
TitleIcosahedrally-averaged bacteriophage Sf6 virion
Map dataicosahedral reconstruction of phage Sf6 virion
Sample
  • Sample: phage Sf6 virion
  • Virus: Shigella phage Sf6 (virus)
Biological speciesShigella phage Sf6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsParent KN / Gilcrease EB / Casjens SR / Baker TS / Tang J
CitationJournal: Virology / Year: 2012
Title: Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures.
Authors: Kristin N Parent / Eddie B Gilcrease / Sherwood R Casjens / Timothy S Baker /
Abstract: Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig- ...Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.
History
DepositionJul 25, 2013-
Header (metadata) releaseAug 7, 2013-
Map releaseAug 7, 2013-
UpdateAug 28, 2013-
Current statusAug 28, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5728_1.png

Downloads & links

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Map

FileDownload / File: emd_5728.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedral reconstruction of phage Sf6 virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 801 pix.
= 857.07 Å		1.07 Å/pix.
x 801 pix.
= 857.07 Å		1.07 Å/pix.
x 801 pix.
= 857.07 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-4.39240313 - 8.890862459999999
Average (Standard dev.)0.08680556 (±0.79273534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions801801801
Spacing801801801
CellA=B=C: 857.07007 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z801801801
origin x/y/z0.0000.0000.000
length x/y/z857.070857.070857.070
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS801801801
D min/max/mean-4.3928.8910.087

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Supplemental data

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Sample components

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Entire : phage Sf6 virion

EntireName: phage Sf6 virion
Components
  • Sample: phage Sf6 virion
  • Virus: Shigella phage Sf6 (virus)

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Supramolecule #1000: phage Sf6 virion

SupramoleculeName: phage Sf6 virion / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Shigella phage Sf6

SupramoleculeName: Shigella phage Sf6 / type: virus / ID: 1 / NCBI-ID: 10761 / Sci species name: Shigella phage Sf6 / Sci species strain: clear mutant / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri (bacteria) / Strain: PE577 / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / T number (triangulation number): 7

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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

Concentration10 mg/mL
BufferpH: 7.6 / Details: 10mM Tris, 10mM MgCl2
GridDetails: 400 mesh Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 5 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 89 K / Max: 91 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at high magnification
DateSep 30, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.07 µm / Number real images: 469 / Average electron dose: 22 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.95 µm / Nominal defocus min: 0.53 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Detailsthe reconstruction was performed with Auto3dem.
CTF correctionDetails: Robem
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 15483

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