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- EMDB-5003: Icosahedral structure of bacteriophage epsilon15 at 4.5 Angstrom ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5003
TitleIcosahedral structure of bacteriophage epsilon15 at 4.5 Angstrom resolution
Map dataIcosahedral reconstruction of bacteriophage Epsilon15 at 4.5 Angstrom resolution
Sample
  • Sample: bacteriophage epsilon15
  • Virus: epsilon15 (virus)
Keywordsbacteriophage / virus / epsilon15 / de novo model / gp7 / gp10 / icosahedral
Function / homology: / Major coat protein-like / : / Major capsid protein GP7 / viral capsid, decoration / viral capsid / Major coat protein / Major capsid protein
Function and homology information
Biological speciesepsilon15 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsJiang W / Baker ML / Jakana J / Weigele PR / King J / Chiu W
CitationJournal: Nature / Year: 2008
Title: Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy.
Authors: Wen Jiang / Matthew L Baker / Joanita Jakana / Peter R Weigele / Jonathan King / Wah Chiu /
Abstract: A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been ...A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-A resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (epsilon15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle's stability. Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states.
History
DepositionJan 29, 2008-
Header (metadata) releaseFeb 28, 2008-
Map releaseApr 14, 2009-
UpdateMar 28, 2011-
Current statusMar 28, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j40
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j40
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j40
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5003_1.png

Downloads & links

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Map

FileDownload / File: emd_5003.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of bacteriophage Epsilon15 at 4.5 Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 768 pix.
= 814.08 Å		1.06 Å/pix.
x 768 pix.
= 814.08 Å		1.06 Å/pix.
x 768 pix.
= 814.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.0265433 - 0.0398315
Average (Standard dev.)0.0000334815 (±0.00215055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-384-384-384
Dimensions768768768
Spacing768768768
CellA=B=C: 814.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z814.080814.080814.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-384-384-384
NC/NR/NS768768768
D min/max/mean-0.0270.0400.000

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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: epsilon15 (virus)

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Supramolecule #1000: bacteriophage epsilon15

SupramoleculeName: bacteriophage epsilon15 / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightExperimental: 22 MDa

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Supramolecule #1: epsilon15

SupramoleculeName: epsilon15 / type: virus / ID: 1 / Name.synonym: epsilon15 / Sci species name: epsilon15 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: epsilon15
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Anatum (bacteria)
synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 22 MDa
Virus shellShell ID: 1 / 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: 50 mM Tris pH7.5, 25 mM NaCl and 10 mM MgCl2
GridDetails: Quantifoil R2/2 grid
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeJEOL 3000SFF
TemperatureAverage: 4.2 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1235 / Average electron dose: 25 e/Å2 / Bits/pixel: 14
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Topentry / Specimen holder model: GATAN HELIUM

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Image processing

CTF correctionDetails: per particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 36259

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