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- EMDB-5724: Bacteriophage Sf6 procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5724
TitleBacteriophage Sf6 procapsid
Map datasf6 procapsid icosahedral reconstruction
Sample
  • Sample: Bacteriophage Sf6 procapsid
  • Virus: Shigella phage Sf6 (virus)
Keywordsicosahedral reconstruction of bacteriophage Sf6 procapsids
Biological speciesShigella phage Sf6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 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: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5724_1.png

Downloads & links

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Map

FileDownload / File: emd_5724.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsf6 procapsid icosahedral reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 761 pix.
= 814.27 Å		1.07 Å/pix.
x 761 pix.
= 814.27 Å		1.07 Å/pix.
x 761 pix.
= 814.27 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: 2.0 / Movie #1: 2
Minimum - Maximum-4.4633193 - 7.98079062
Average (Standard dev.)0.0360463 (±0.71626443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-380-380-380
Dimensions761761761
Spacing761761761
CellA=B=C: 814.27 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z761761761
origin x/y/z0.0000.0000.000
length x/y/z814.270814.270814.270
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-380-380-380
NC/NR/NS761761761
D min/max/mean-4.4637.9810.036

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Supplemental data

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Sample components

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Entire : Bacteriophage Sf6 procapsid

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

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Supramolecule #1000: Bacteriophage Sf6 procapsid

SupramoleculeName: Bacteriophage Sf6 procapsid / 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 / Details: This is a precursor procapsid. / NCBI-ID: 10761 / Sci species name: Shigella phage Sf6 / Sci species strain: clear plaque mutant / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri (bacteria) / Strain: PE577 / synonym: BACTERIA(EUBACTERIA)

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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

Concentration8 mg/mL
BufferpH: 7.6 / Details: 10mM Tris, 10mM MgCl2
GridDetails: 400 mesh Quantifoil R2/2, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 5 sec 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
DateApr 19, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.07 µm / Number real images: 139 / 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: 4.61 µm / Nominal defocus min: 0.58 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 done using AUTO3DEM
CTF correctionDetails: Robem
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem
Details: The particles were selected and preprocessed using RobEM. Image reconstruction was performed using Auto3DEM.
Number images used: 6851

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