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- EMDB-5217: Visualizing the structural changes of bacteriophage epsilon15 and... -

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Basic information

Entry
Database: EMDB / ID: 5217
TitleVisualizing the structural changes of bacteriophage epsilon15 and its Salmonella host during infection
Map dataEmpty capsid attached to cell
SampleBacteriophage epsilon15, Salmonella anatum:
virus
Keywordsvirus / infection / Salmonella / tomography / bacteriophage
Sourceepsilon15 (bacteriophage)
Methodsubtomogram averaging / cryo EM
AuthorsChang JT / Schmid MF / Haase-Pettingell C / Weigele PR / King JA / Chiu W
CitationJournal: J. Mol. Biol. / Year: 2010
Title: Visualizing the structural changes of bacteriophage Epsilon15 and its Salmonella host during infection.
Authors: Juan T Chang / Michael F Schmid / Cameron Haase-Pettingell / Peter R Weigele / Jonathan A King / Wah Chiu
Abstract: The efficient mechanism by which double-stranded DNA bacteriophages deliver their chromosome across the outer membrane, cell wall, and inner membrane of Gram-negative bacteria remains obscure. ...The efficient mechanism by which double-stranded DNA bacteriophages deliver their chromosome across the outer membrane, cell wall, and inner membrane of Gram-negative bacteria remains obscure. Advances in single-particle electron cryomicroscopy have recently revealed details of the organization of the DNA injection apparatus within the mature virion for various bacteriophages, including epsilon15 (ɛ15) and P-SSP7. We have used electron cryotomography and three-dimensional subvolume averaging to capture snapshots of ɛ15 infecting its host Salmonella anatum. These structures suggest the following stages of infection. In the first stage, the tailspikes of ɛ15 attach to the surface of the host cell. Next, ɛ15's tail hub attaches to a putative cell receptor and establishes a tunnel through which the injection core proteins behind the portal exit the virion. A tube spanning the periplasmic space is formed for viral DNA passage, presumably from the rearrangement of core proteins or from cellular components. This tube would direct the DNA into the cytoplasm and protect it from periplasmic nucleases. Once the DNA has been injected into the cell, the tube and portal seals, and the empty bacteriophage remains at the cell surface.
DateDeposition: Jul 22, 2010 / Header (metadata) release: Aug 4, 2010 / Map release: Oct 11, 2010 / Last update: Sep 12, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5217.map.gz (map file in CCP4 format, 27649 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
10.8 Å/pix.
= 2073.6 Å
192 pix
10.8 Å/pix.
= 2073.6 Å
192 pix
10.8 Å/pix.
= 2073.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.8 Å
Density
Contour Level:0.11 (by author), 0.11 (movie #1):
Minimum - Maximum-0.248063 - 0.41223
Average (Standard dev.)2.08952e-05 (0.0354595)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 2073.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.810.810.8
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z2073.6002073.6002073.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2480.4120.000

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Supplemental data

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Sample components

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Entire Bacteriophage epsilon15, Salmonella anatum

EntireName: Bacteriophage epsilon15, Salmonella anatum / Number of components: 2

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Component #1: virus, epsilon15

VirusName: epsilon15Epsilon 15 / a.k.a: epsilon15Epsilon 15 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: epsilon15 (bacteriophage)
Source (natural)Host Species: Salmonella enterica subsp. enterica serovar Anatum
Host category: BACTERIA(EUBACTERIA)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Support film200 mesh copper grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 100 % / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Date: Sep 16, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 20000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 6000 - 9000 nm / Energy filter: JEM3200FSC / Energy window: 0-20 eV
Specimen HolderHolder: Eucentric / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 93 K ( 93 - 93 K)
CameraDetector: GENERIC CCD

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Image processing

ProcessingMethod: subtomogram averaging
3D reconstructionDetails: The 3D reconstructions were performed with IMOD using gold as fiducial markers. Subvolumes, each containing a single particle, were computationally extracted from the reconstructions, aligned to a reference model, and averaged together.

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