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- EMDB-1176: Structure of epsilon15 bacteriophage reveals genome organization ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1176
TitleStructure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.
Map data3-fold view of icosahedral symmetry imposed capsid shell map
Sample
  • Sample: Bacteriophage Epsilon15
  • Virus: Salmonella phage epsilon15 (virus)
Biological speciesSalmonella phage epsilon15 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsJiang W / Chang J / Jakana J / Weigele P / King J / Chiu W
CitationJournal: Nature / Year: 2006
Title: Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.
Authors: Wen Jiang / Juan Chang / Joanita Jakana / Peter Weigele / Jonathan King / Wah Chiu /
Abstract: The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. ...The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. These component structures do not share icosahedral symmetry and cannot be resolved using a conventional icosahedral averaging method. Here we report the structure of the entire infectious Salmonella bacteriophage epsilon15 (ref. 1) determined from single-particle cryo-electron microscopy, without icosahedral averaging. This structure displays not only the icosahedral shell of 60 hexamers and 11 pentamers, but also the non-icosahedral components at one pentameric vertex. The densities at this vertex can be identified as the 12-subunit portal complex sandwiched between an internal cylindrical core and an external tail hub connecting to six projecting trimeric tailspikes. The viral genome is packed as coaxial coils in at least three outer layers with approximately 90 terminal nucleotides extending through the protein core and the portal complex and poised for injection. The shell protein from icosahedral reconstruction at higher resolution exhibits a similar fold to that of other double-stranded DNA viruses including herpesvirus, suggesting a common ancestor among these diverse viruses. The image reconstruction approach should be applicable to studying other biological nanomachines with components of mixed symmetries.
History
DepositionNov 3, 2005-
Header (metadata) releaseNov 3, 2005-
Map releaseNov 3, 2006-
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: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1176.gif

Downloads & links

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Map

FileDownload / File: emd_1176.map.gz / Format: CCP4 / Size: 202.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3-fold view of icosahedral symmetry imposed capsid shell map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 239 pix.
= 380.01 Å		1.59 Å/pix.
x 477 pix.
= 758.43 Å		1.59 Å/pix.
x 477 pix.
= 758.43 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: 1.59 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.67 / Movie #1: 2
Minimum - Maximum-9.582420000000001 - 10.147
Average (Standard dev.)0.0000000017426 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-238-238-119
Dimensions477477239
Spacing477477239
CellA: 758.43 Å / B: 758.43 Å / C: 380.01 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.591.591.59
M x/y/z477477239
origin x/y/z0.0000.0000.000
length x/y/z758.430758.430380.010
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-770
NX/NY/NZ15515578
MAP C/R/S123
start NC/NR/NS-238-238-119
NC/NR/NS477477239
D min/max/mean-9.58210.1470.000

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Supplemental data

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Sample components

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Entire : Bacteriophage Epsilon15

EntireName: Bacteriophage Epsilon15
Components
  • Sample: Bacteriophage Epsilon15
  • Virus: Salmonella phage epsilon15 (virus)

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Supramolecule #1000: Bacteriophage Epsilon15

SupramoleculeName: Bacteriophage Epsilon15 / type: sample / ID: 1000 / Details: icosahedral shell structure / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightTheoretical: 500 KDa

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Supramolecule #1: Salmonella phage epsilon15

SupramoleculeName: Salmonella phage epsilon15 / type: virus / ID: 1 / NCBI-ID: 215158 / Sci species name: Salmonella phage epsilon15 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: shell / Diameter: 700 Å / T number (triangulation number): 7
Virus shellShell ID: 2 / Name: shell / Diameter: 700 Å / T number (triangulation number): 7
Virus shellShell ID: 3 / Name: shell / Diameter: 700 Å / T number (triangulation number): 7

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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

BufferpH: 7.5 / Details: 10 mM Tris pH7.5, 25 mM NaCl and 5 mM MgCl2
GridDetails: Quantifoil R2/2 grid
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeJEOL 3000SFF
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Topentry / Specimen holder model: OTHER
TemperatureAverage: 4.2 K
DateOct 10, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 200 / Average electron dose: 25 e/Å2 / Details: Scanned by Nikon CoolScan 9000ED / Bits/pixel: 14

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Image processing

CTF correctionDetails: per particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SAVR / Number images used: 6000

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