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- EMDB-1280: Cryo-electron microscopy study of bacteriophage T4 displaying ant... -

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Entry
Database: EMDB / ID: EMD-1280
TitleCryo-electron microscopy study of bacteriophage T4 displaying anthrax toxin proteins.
Map dataBacteriophage T4 capsid decorated with anthrax toxin proteins. N-terminal domain of the anhrax lethal factor (nLF) was fused with T4 Soc protein. nLF-Soc molecules were attached to the surface of Hoc-minus Soc-minus T4 phage mutant. Then the anthrax protective antigen, PA63, heptamers were attached to the capsid-exposed LFn domains.
Sample
  • Sample: Bacteriophage T4 decorated with anthrax toxin proteins
  • Virus: Enterobacteria phage T4 (virus)
  • Protein or peptide: LFn-Soc fusion protein
  • Protein or peptide: anthrax PA63
Biological speciesBacillus anthracis (anthrax bacterium) / Enterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 35.0 Å
AuthorsFokine A / Bowman VD / Battisti AJ / Li Q / Chipman PR / Rao VB / Rossmann MG
CitationJournal: Virology / Year: 2007
Title: Cryo-electron microscopy study of bacteriophage T4 displaying anthrax toxin proteins.
Authors: Andrei Fokine / Valorie D Bowman / Anthony J Battisti / Qin Li / Paul R Chipman / Venigalla B Rao / Michael G Rossmann /
Abstract: The bacteriophage T4 capsid contains two accessory surface proteins, the small outer capsid protein (Soc, 870 copies) and the highly antigenic outer capsid protein (Hoc, 155 copies). As these are ...The bacteriophage T4 capsid contains two accessory surface proteins, the small outer capsid protein (Soc, 870 copies) and the highly antigenic outer capsid protein (Hoc, 155 copies). As these are dispensable for capsid formation, they can be used for displaying proteins and macromolecular complexes on the T4 capsid surface. Anthrax toxin components were attached to the T4 capsid as a fusion protein of the N-terminal domain of the anthrax lethal factor (LFn) with Soc. The LFn-Soc fusion protein was complexed in vitro with Hoc(-)Soc(-)T4 phage. Subsequently, cleaved anthrax protective antigen heptamers (PA63)(7) were attached to the exposed LFn domains. A cryo-electron microscopy study of the decorated T4 particles shows the complex of PA63 heptamers with LFn-Soc on the phage surface. Although the cryo-electron microscopy reconstruction is unable to differentiate on its own between different proposed models of the anthrax toxin, the density is consistent with a model that had predicted the orientation and position of three LFn molecules bound to one PA63 heptamer.
History
DepositionJul 7, 2006-
Header (metadata) releaseOct 20, 2006-
Map releaseOct 3, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1280.gif

Downloads & links

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Map

FileDownload / File: emd_1280.map.gz / Format: CCP4 / Size: 78.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage T4 capsid decorated with anthrax toxin proteins. N-terminal domain of the anhrax lethal factor (nLF) was fused with T4 Soc protein. nLF-Soc molecules were attached to the surface of Hoc-minus Soc-minus T4 phage mutant. Then the anthrax protective antigen, PA63, heptamers were attached to the capsid-exposed LFn domains.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.96 Å/pix.
x 276 pix.
= 1644.96 Å		5.96 Å/pix.
x 276 pix.
= 1644.96 Å		5.96 Å/pix.
x 276 pix.
= 1644.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.96 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.332 / Movie #1: 0.09
Minimum - Maximum-0.728074 - 0.673265
Average (Standard dev.)0.0255938 (±0.120915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-138-138-138
Dimensions276276276
Spacing276276276
CellA=B=C: 1644.96 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.965.965.96
M x/y/z276276276
origin x/y/z0.0000.0000.000
length x/y/z1644.9601644.9601644.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-138-138-138
NC/NR/NS276276276
D min/max/mean-0.7280.6730.026

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Supplemental data

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Sample components

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Entire : Bacteriophage T4 decorated with anthrax toxin proteins

EntireName: Bacteriophage T4 decorated with anthrax toxin proteins
Components
  • Sample: Bacteriophage T4 decorated with anthrax toxin proteins
  • Virus: Enterobacteria phage T4 (virus)
  • Protein or peptide: LFn-Soc fusion protein
  • Protein or peptide: anthrax PA63

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Supramolecule #1000: Bacteriophage T4 decorated with anthrax toxin proteins

SupramoleculeName: Bacteriophage T4 decorated with anthrax toxin proteins
type: sample / ID: 1000
Details: Bacteriophage T4 decorated with anthrax toxin proteins. N-terminal domain of the anhrax lethal factor (nLF) was fused with T4 Soc protein. nLF-Soc molecules were attached to the surface of ...Details: Bacteriophage T4 decorated with anthrax toxin proteins. N-terminal domain of the anhrax lethal factor (nLF) was fused with T4 Soc protein. nLF-Soc molecules were attached to the surface of Hoc-minus Soc-minus T4 phage mutant. Then the anthrax protective antigen, PA63, heptamers were attached to the capsid-exposed LFn domains.
Number unique components: 3

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: E.coli (others) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid shell / Diameter: 1200 Å / T number (triangulation number): 20
Virus shellShell ID: 2 / Diameter: 850 Å / T number (triangulation number): 13

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Macromolecule #1: LFn-Soc fusion protein

MacromoleculeName: LFn-Soc fusion protein / type: protein_or_peptide / ID: 1 / Number of copies: 700 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Bacillus anthracis (anthrax bacterium) / synonym: Bacillus Anthracis
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: anthrax PA63

MacromoleculeName: anthrax PA63 / type: protein_or_peptide / ID: 2 / Number of copies: 700 / Oligomeric state: heptamer / Recombinant expression: Yes
Source (natural)Organism: Bacillus anthracis (anthrax bacterium) / synonym: Bacillus Anthracis

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: in house manufactured / Method: hand blot 3 seconds, plunging during blot

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Alignment procedureLegacy - Astigmatism: live fft at 190,000x
DateFeb 12, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 50 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider
Details: The reconstruction was performed imposing D5 symmetry
Number images used: 722

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