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- EMDB-1392: A three-dimensional cryo-electron microscopy structure of the bac... -

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Basic information

Entry
Database: EMDB / ID: EMD-1392
TitleA three-dimensional cryo-electron microscopy structure of the bacteriophage phiKZ head.
Map datacryo-EM reconstruction of the bacteriophage phiKZ capsid
Sample
  • Sample: Bacteriophage phiKZ capsid
  • Virus: Pseudomonas phage phiKZ (virus)
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsFokine A / Kostyuchenko V / Efimov A / Kurochkina L / Sykilinda N / Robben J / Volckaert G / Hoenger A / Chipman P / Battisti A ...Fokine A / Kostyuchenko V / Efimov A / Kurochkina L / Sykilinda N / Robben J / Volckaert G / Hoenger A / Chipman P / Battisti A / Rossmann M / Mesyanzhinov V
CitationJournal: J Mol Biol / Year: 2005
Title: A three-dimensional cryo-electron microscopy structure of the bacteriophage phiKZ head.
Authors: Andrei Fokine / Victor A Kostyuchenko / Andrey V Efimov / Lidia P Kurochkina / Nina N Sykilinda / Johan Robben / Guido Volckaert / Andreas Hoenger / Paul R Chipman / Anthony J Battisti / ...Authors: Andrei Fokine / Victor A Kostyuchenko / Andrey V Efimov / Lidia P Kurochkina / Nina N Sykilinda / Johan Robben / Guido Volckaert / Andreas Hoenger / Paul R Chipman / Anthony J Battisti / Michael G Rossmann / Vadim V Mesyanzhinov /
Abstract: The three-dimensional structure of the Pseudomonas aeruginosa bacteriophage phiKZ head has been determined by cryo-electron microscopy and image reconstruction to 18A resolution. The head has ...The three-dimensional structure of the Pseudomonas aeruginosa bacteriophage phiKZ head has been determined by cryo-electron microscopy and image reconstruction to 18A resolution. The head has icosahedral symmetry measuring 1455 A in diameter along 5-fold axes and a unique portal vertex to which is attached an approximately 1800 A-long contractile tail. The 65 kDa major capsid protein, gp120, is organized into a surface lattice of hexamers, with T = 27 triangulation. The shape and size of the hexamers is similar to the hexameric building blocks of the bacteriophages T4, phi29, P22, and HK97. Pentameric vertices of the capsid are occupied by complexes composed of several special vertex proteins. The double-stranded genomic DNA is packaged into a highly condensed series of layers, separated by 24 A, that follow the contour of the inner wall of the capsid.
History
DepositionJul 16, 2007-
Header (metadata) releaseJul 17, 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: 0.054496524
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.054496524
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1392.gif

emd_1392.tif

Downloads & links

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Map

FileDownload / File: emd_1392.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM reconstruction of the bacteriophage phiKZ capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 360 pix.
= 1527.12 Å		4.24 Å/pix.
x 360 pix.
= 1527.12 Å		4.24 Å/pix.
x 360 pix.
= 1527.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.242 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0662 / Movie #1: 0.0544965
Minimum - Maximum-0.126409 - 0.210199
Average (Standard dev.)0.0141981 (±0.0326387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1527.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.2424.2424.242
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z1527.1201527.1201527.120
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/NS360360360
D min/max/mean-0.1260.2100.014

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Supplemental data

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Sample components

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Entire : Bacteriophage phiKZ capsid

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

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Supramolecule #1000: Bacteriophage phiKZ capsid

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

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Name.synonym: phage phiKZ head, bacteriophage phiKZ / NCBI-ID: 169683 / Sci species name: Pseudomonas phage phiKZ / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: phage phiKZ head, bacteriophage phiKZ
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gp120 / Diameter: 1455 Å / T number (triangulation number): 27

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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, pluging 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 / 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: 92 / Average electron dose: 20 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: each particle
Final angle assignmentDetails: SPIDER theta 37 degrees phi 72 degrees
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: SPIDER
Details: reconstruction was performed using the icosahedral symmetry
Number images used: 2000

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