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- EMDB-1268: Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. -

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Basic information

Entry
Database: EMDB / ID: EMD-1268
TitleStructure of bacteriophage SPP1 tail reveals trigger for DNA ejection.
Map dataCCP4 map of the helical Tail of the bacteriophage SPP1 after DNA ejection
Sample
  • Sample: Tail of the bacteriophage SPP1 after DNa ejection
  • Protein or peptide: Major Tail Protein 1
  • Protein or peptide: Major Tail Protein 2
Biological speciesBacillus phage SPP1 (virus)
Methodhelical reconstruction / negative staining / Resolution: 14.5 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
DepositionAug 14, 2006-
Header (metadata) releaseSep 18, 2006-
Map releaseSep 7, 2007-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.754398916
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.754398916
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1268.gif

Downloads & links

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Map

FileDownload / File: emd_1268.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCCP4 map of the helical Tail of the bacteriophage SPP1 after DNA ejection
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 128 pix.
= 179.2 Å		1.4 Å/pix.
x 128 pix.
= 179.2 Å		1.4 Å/pix.
x 128 pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.22 / Movie #1: 0.7543989
Minimum - Maximum0.0 - 6.72672
Average (Standard dev.)0.178862 (±0.551362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 179.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean0.0006.7270.179

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Supplemental data

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Sample components

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Entire : Tail of the bacteriophage SPP1 after DNa ejection

EntireName: Tail of the bacteriophage SPP1 after DNa ejection
Components
  • Sample: Tail of the bacteriophage SPP1 after DNa ejection
  • Protein or peptide: Major Tail Protein 1
  • Protein or peptide: Major Tail Protein 2

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Supramolecule #1000: Tail of the bacteriophage SPP1 after DNa ejection

SupramoleculeName: Tail of the bacteriophage SPP1 after DNa ejection / type: sample / ID: 1000 / Oligomeric state: hexameric rings of gp17.1 and gp17.1star / Number unique components: 2

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Macromolecule #1: Major Tail Protein 1

MacromoleculeName: Major Tail Protein 1 / type: protein_or_peptide / ID: 1 / Name.synonym: gp17.1
Details: The 180 nm-long tail tube is composed of the two major tail proteins, gp17.1 and gp17.1star. They form a helical stack of 45 rings.
Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bacillus phage SPP1 (virus) / synonym: Bacteriophage SPP1
Molecular weightExperimental: 19.1 KDa

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Macromolecule #2: Major Tail Protein 2

MacromoleculeName: Major Tail Protein 2 / type: protein_or_peptide / ID: 2 / Name.synonym: gp17.1star / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bacillus phage SPP1 (virus) / synonym: Bacteriophage SPP1
Molecular weightExperimental: 28.2 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5 / Details: 50 mM Tris-Cl, 300 mM NaCl, 5 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 F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / 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: 50000
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 100,000 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: 12 / Average electron dose: 10 e/Å2 / Od range: 2.5 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipping
Final angle assignmentDetails: IMAGIC beta range 65-115 degrees, gamma range 0-60 degrees
Final reconstructionApplied symmetry - Helical parameters - Δz: 40 Å
Applied symmetry - Helical parameters - Δ&Phi: 21 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER / Details: exact filter back-projection

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