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- EMDB-1393: Cryo-EM study of the Pseudomonas bacteriophage phiKZ. -

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Basic information

Entry
Database: EMDB / ID: EMD-1393
TitleCryo-EM study of the Pseudomonas bacteriophage phiKZ.
Map dataCryoEM reconstruction of the bacteriophage phiKZ baseplate an a part of the tail sheath
Sample
  • Sample: Bacteriophage phiKZ
  • Virus: Pseudomonas phage phiKZ (virus)
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsFokine A / Battisti A / Bowman V / Efimov A / Kurochkina L / Chipman P / Mesyanzhinov V / Rossmann M
CitationJournal: Structure / Year: 2007
Title: Cryo-EM study of the Pseudomonas bacteriophage phiKZ.
Authors: Andrei Fokine / Anthony J Battisti / Valorie D Bowman / Andrei V Efimov / Lidia P Kurochkina / Paul R Chipman / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The phiKZ virus is one of the largest known bacteriophages. It infects Pseudomonas aeruginosa, which is frequently pathogenic in humans, and, therefore, has potential for phage therapy. The phiKZ ...The phiKZ virus is one of the largest known bacteriophages. It infects Pseudomonas aeruginosa, which is frequently pathogenic in humans, and, therefore, has potential for phage therapy. The phiKZ virion consists of an approximately 1450 A diameter icosahedral head and an approximately 2000 A long contractile tail. The structure of the phiKZ tail has been determined using cryo-electron microscopy. The phiKZ tail is much longer than that of bacteriophage T4. However, the helical parameters of their contractile sheaths, surrounding their tail tubes, are comparable. Although there is no recognizable sequence similarity between the phiKZ and T4 tail sheath proteins, they are similar in size and shape, suggesting that they evolved from a common ancestor. The phiKZ baseplate is significantly larger than that of T4 and has a flatter shape. Nevertheless, phiKZ, similar to T4, has a cell-puncturing device in the middle of its baseplate.
History
DepositionJul 23, 2007-
Header (metadata) releaseJul 23, 2007-
Map releaseSep 6, 2007-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1393.gif

Downloads & links

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Map

FileDownload / File: emd_1393.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of the bacteriophage phiKZ baseplate an a part of the tail sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.48 Å/pix.
x 96 pix.
= 814.08 Å		8.48 Å/pix.
x 96 pix.
= 814.08 Å		8.48 Å/pix.
x 96 pix.
= 814.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.48 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.295 / Movie #1: 0.3
Minimum - Maximum-0.60063 - 1.70702
Average (Standard dev.)0.0120705 (±0.1335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 814.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.488.488.48
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z814.080814.080814.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.6011.7070.012

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Supplemental data

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Sample components

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Entire : Bacteriophage phiKZ

EntireName: Bacteriophage phiKZ
Components
  • Sample: Bacteriophage phiKZ
  • Virus: Pseudomonas phage phiKZ (virus)

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Supramolecule #1000: Bacteriophage phiKZ

SupramoleculeName: Bacteriophage phiKZ / type: sample / ID: 1000 / Oligomeric state: one / Number unique components: 1

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Name.synonym: phiKZ baseplate, tail / NCBI-ID: 169683 / Sci species name: Pseudomonas phage phiKZ / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: phiKZ baseplate, tail
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / 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

BufferpH: 7.5 / Details: 50 mM tris-Acetate-EDTA buffer (pH 7.5)
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: in house manufactured / Method: hand blot 3 seconds, plugging during blot

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Alignment procedureLegacy - Astigmatism: live fft
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 112 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: The reconstruction was calculated assuming the 6-fold symmetry.
Number images used: 1112

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