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- EMDB-1175: Structure of epsilon15 bacteriophage reveals genome organization ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1175
TitleStructure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.
Map dataDensity map of Epsilon15 phage
Sample
  • Sample: Bacteriophage Epsilon15
  • Virus: Salmonella phage epsilon15 (virus)
  • Protein or peptide: portal
  • Protein or peptide: tailspike
  • Protein or peptide: tail hub
  • Protein or peptide: core
  • DNA: dsDNA genome
Biological speciesSalmonella phage epsilon15 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 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 2, 2005-
Header (metadata) releaseNov 3, 2005-
Map releaseNov 3, 2006-
UpdateOct 3, 2012-
Current statusOct 3, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1175.gif

Downloads & links

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Map

FileDownload / File: emd_1175.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of Epsilon15 phage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.08 Å/pix.
x 288 pix.
= 1175.04 Å		4.08 Å/pix.
x 288 pix.
= 1175.04 Å		4.08 Å/pix.
x 288 pix.
= 1175.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.08 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.467 / Movie #1: 0.5
Minimum - Maximum-1.78221 - 1.96078
Average (Standard dev.)0.00880378 (±0.236622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-144-144-144
Dimensions288288288
Spacing288288288
CellA=B=C: 1175.04 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.084.084.08
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1175.0401175.0401175.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-770
NX/NY/NZ15515578
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
D min/max/mean-1.7821.9610.009

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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)
  • Protein or peptide: portal
  • Protein or peptide: tailspike
  • Protein or peptide: tail hub
  • Protein or peptide: core
  • DNA: dsDNA genome

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Supramolecule #1000: Bacteriophage Epsilon15

SupramoleculeName: Bacteriophage Epsilon15 / type: sample / ID: 1000
Details: intact Epsilon15 phage particle with both icosahedral and non-icosahedral components
Oligomeric state: icosahedral shell and12 fold portal and 6 fold tail and internal core and dsDNA genome
Number unique components: 6
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)

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Macromolecule #1: portal

MacromoleculeName: portal / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Oligomeric state: 12 / Recombinant expression: No
Source (natural)Organism: Salmonella phage epsilon15 (virus)

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Macromolecule #2: tailspike

MacromoleculeName: tailspike / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Oligomeric state: 3 / Recombinant expression: No
Source (natural)Organism: Salmonella phage epsilon15 (virus)

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Macromolecule #3: tail hub

MacromoleculeName: tail hub / type: protein_or_peptide / ID: 3 / Recombinant expression: No
Source (natural)Organism: Salmonella phage epsilon15 (virus)

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Macromolecule #4: core

MacromoleculeName: core / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: Salmonella phage epsilon15 (virus)

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Macromolecule #5: dsDNA genome

MacromoleculeName: dsDNA genome / type: dna / ID: 5 / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Salmonella phage epsilon15 (virus)

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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 2010F
TemperatureAverage: 100 K
Detailsimaged using JAMES software
DateDec 18, 2004
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 950 / Average electron dose: 10 e/Å2 / Details: Direct recording on Gatan 4k CCD / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: per particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SAVR / Number images used: 15000

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