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

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Basic information

Database: EMDB / ID: 1269
TitleStructure of bacteriophage SPP1 tail reveals trigger for DNA ejection.
Map dataccp4 map of the tip of the bacteriophage spp1
SampleTip of the Tail of the bacteriophage SPP1:
interface tail-tip / tip fiber
SourceBacillus phage SPP1 (bacteriophage)
Methodsingle particle reconstruction / negative staining / 20 Å resolution
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
DateDeposition: Sep 21, 2006 / Header (metadata) release: Sep 22, 2006 / Map release: Sep 7, 2007 / Last update: Dec 11, 2013

Structure visualization

  • 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
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_1269.map.gz (map file in CCP4 format, 3251 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
3.3 Å/pix.
= 429. Å
80 pix
3.3 Å/pix.
= 264. Å
80 pix
3.3 Å/pix.
= 264. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Contour Level:0.00819 (by author), 0.008487 (movie #1):
Minimum - Maximum-0.00608738 - 0.15806589
Average (Standard dev.)0.00082439 (0.00736948)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 264 Å / B: 264 Å / C: 429 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-184-184-183
MAP C/R/S123
start NC/NR/NS818161
D min/max/mean-0.0060.1580.001

Supplemental data

Sample components

Entire Tip of the Tail of the bacteriophage SPP1

EntireName: Tip of the Tail of the bacteriophage SPP1
Details: The total number of proteins that compose the tail Tip is still under investigation.
Number of components: 2

Component #1: protein, interface tail-tip

ProteinName: interface tail-tip / a.k.a: gp19.1 / Recombinant expression: No
MassExperimental: 28.5 kDa
SourceSpecies: Bacillus phage SPP1 (bacteriophage)

Component #2: protein, tip fiber

ProteinName: tip fiber / a.k.a: gp21 / Recombinant expression: No
MassExperimental: 123 kDa
SourceSpecies: Bacillus phage SPP1 (bacteriophage)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionBuffer solution: 100 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2 / pH: 7.5
Support film300 mesh copper grid
Staining3.5 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.
VitrificationCryogen name: NONE

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Details: Low Dose Imaging
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal), 43475 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2000 nm
Specimen HolderHolder: Gatan single tilt negative stain holder / Model: OTHER / Temperature: 298 K
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 20 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 2.5

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 364 / Applied symmetry: C3 (3 fold cyclic)
3D reconstructionAlgorithm: angular reconstitution / Software: IMAGIC
Details: The 3D reconstruction has been caried out using a C3 symmetry and the exact-filter back projection method.
Resolution: 20 Å / Resolution method: FSC 0.5

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