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- EMDB-1415: Cryo-EM study of the Pseudomonas bacteriophage phiKZ. -

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Basic information

Entry
Database: EMDB / ID: EMD-1415
TitleCryo-EM study of the Pseudomonas bacteriophage phiKZ.
Map dataThis is a 3D model of the bacteriophage phiKZ based on the previously deposited reconstructions of the capsid (EMD-1392) and the tail (EMD-1393)
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
DepositionAug 30, 2007-
Header (metadata) releaseAug 30, 2007-
Map releaseAug 30, 2007-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1415.gif

Downloads & links

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Map

FileDownload / File: emd_1415.map.gz / Format: CCP4 / Size: 48.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3D model of the bacteriophage phiKZ based on the previously deposited reconstructions of the capsid (EMD-1392) and the tail (EMD-1393)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.48 Å/pix.
x 400 pix.
= 3393.92 Å		8.48 Å/pix.
x 180 pix.
= 1527.264 Å		8.48 Å/pix.
x 180 pix.
= 1527.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.4848 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.303 / Movie #1: 0.3
Minimum - Maximum-0.598439 - 1.00275
Average (Standard dev.)0.0350662 (±0.121433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-200
Dimensions180180400
Spacing180180400
CellA: 1527.26 Å / B: 1527.26 Å / C: 3393.92 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.48488.48488.4848
M x/y/z180180400
origin x/y/z0.0000.0000.000
length x/y/z1527.2641527.2643393.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-90
NX/NY/NZ181181181
MAP C/R/S123
start NC/NR/NS-90-90-200
NC/NR/NS180180400
D min/max/mean-0.5981.0030.035

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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 / NCBI-ID: 169683 / Sci species name: Pseudomonas phage phiKZ / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER
Details: This is a model of the phiKZ virion based on the previously deposited reconstructions of the phiKZ capsid and the tail part.

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