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- EMDB-1269: Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. -

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Basic information

Entry
Database: EMDB / ID: EMD-1269
TitleStructure of bacteriophage SPP1 tail reveals trigger for DNA ejection.
Map dataccp4 map of the tip of the bacteriophage spp1
Sample
  • Sample: Tip of the Tail of the bacteriophage SPP1
  • Protein or peptide: interface tail-tip
  • Protein or peptide: tip fiber
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsPlisson C / White HE / Auzat I / Sao-jose C / Lhuillier S / Tavares P / Orlova EV
CitationJournal: EMBO J / Year: 2007
Title: Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection.
Authors: Celia Plisson / Helen E White / Isabelle Auzat / Amineh Zafarani / Carlos São-José / Sophie Lhuillier / Paulo Tavares / Elena V Orlova /
Abstract: The majority of known bacteriophages have long noncontractile tails (Siphoviridae) that serve as a pipeline for genome delivery into the host cytoplasm. The tail extremity distal from the phage head ...The majority of known bacteriophages have long noncontractile tails (Siphoviridae) that serve as a pipeline for genome delivery into the host cytoplasm. The tail extremity distal from the phage head is an adsorption device that recognises the bacterial receptor at the host cell surface. This interaction generates a signal transmitted to the head that leads to DNA release. We have determined structures of the bacteriophage SPP1 tail before and after DNA ejection. The results reveal extensive structural rearrangements in the internal wall of the tail tube. We propose that the adsorption device-receptor interaction triggers a conformational switch that is propagated as a domino-like cascade along the 1600 A-long helical tail structure to reach the head-to-tail connector. This leads to opening of the connector culminating in DNA exit from the head into the host cell through the tail tube.
History
DepositionSep 21, 2006-
Header (metadata) releaseSep 22, 2006-
Map releaseSep 7, 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: 0.00848698
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00848698
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1269.gif

Downloads & links

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Map

FileDownload / File: emd_1269.map.gz / Format: CCP4 / Size: 3.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationccp4 map of the tip of the bacteriophage spp1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 130 pix.
= 429. Å		3.3 Å/pix.
x 80 pix.
= 264. Å		3.3 Å/pix.
x 80 pix.
= 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: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00819 / Movie #1: 0.008487
Minimum - Maximum-0.00608738 - 0.15806589
Average (Standard dev.)0.00082439 (±0.00736948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin818161
Dimensions8080130
Spacing8080130
CellA: 264.0 Å / B: 264.0 Å / C: 429.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z8080130
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000429.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS818161
NC/NR/NS8080130
D min/max/mean-0.0060.1580.001

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Supplemental data

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Sample components

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Entire : Tip of the Tail of the bacteriophage SPP1

EntireName: Tip of the Tail of the bacteriophage SPP1
Components
  • Sample: Tip of the Tail of the bacteriophage SPP1
  • Protein or peptide: interface tail-tip
  • Protein or peptide: tip fiber

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Supramolecule #1000: Tip of the Tail of the bacteriophage SPP1

SupramoleculeName: Tip of the Tail of the bacteriophage SPP1 / type: sample / ID: 1000
Details: The total number of proteins that compose the tail Tip is still under investigation.
Number unique components: 2

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Macromolecule #1: interface tail-tip

MacromoleculeName: interface tail-tip / type: protein_or_peptide / ID: 1 / Name.synonym: gp19.1 / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / synonym: Bacteriophage SPP1
Molecular weightExperimental: 28.5 KDa

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Macromolecule #2: tip fiber

MacromoleculeName: tip fiber / type: protein_or_peptide / ID: 2 / Name.synonym: gp21 / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / synonym: Bacteriophage SPP1
Molecular weightExperimental: 123 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 100 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2
StainingType: NEGATIVE
Details: 3.5 microliter of sample was applied onto carbon-coated copper grids, which were glow-discharged for 30 seconds. The sample was left for 1-2 minutes on the grids before blotting and staining ...Details: 3.5 microliter of sample was applied onto carbon-coated copper grids, which were glow-discharged for 30 seconds. The sample was left for 1-2 minutes on the grids before blotting and staining with a solution of 2% uranyl acetate.
GridDetails: 300 mesh copper grid
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 43475 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 42000
Sample stageSpecimen holder: Gatan single tilt negative stain holder / Specimen holder model: OTHER
TemperatureAverage: 298 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
DetailsLow Dose Imaging
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 20 / Average electron dose: 10 e/Å2 / Od range: 2.5 / Bits/pixel: 8

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC
Details: The 3D reconstruction has been caried out using a C3 symmetry and the exact-filter back projection method.
Number images used: 364

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