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- EMDB-5203: Subtomogram average of epsilon15 using Zernike phase contrast mic... -

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Basic information

Entry
Database: EMDB / ID: EMD-5203
TitleSubtomogram average of epsilon15 using Zernike phase contrast microscopy
Map dataThis is an image of a surface rendered top-view of epsilon 15 phage reconstructed with 50 subtomograms taken with a Zernike phase plate.
Sample
  • Sample: Epsilon 15
  • Virus: epsilon15 (virus)
KeywordsPhase contrast / cryoEM / electron tomography / bacteriophage
Biological speciesepsilon15 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsMurata K / Liu X / Danev R / Jakana J / Schmid MF / King J / Nagayama K / Chiu W
CitationJournal: Structure / Year: 2010
Title: Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions.
Authors: Kazuyoshi Murata / Xiangan Liu / Radostin Danev / Joanita Jakana / Michael F Schmid / Jonathan King / Kuniaki Nagayama / Wah Chiu /
Abstract: Zernike phase contrast cryo-electron microscopy (ZPC-cryoEM) is an emerging technique that is capable of producing higher image contrast than conventional cryoEM. By combining this technique with ...Zernike phase contrast cryo-electron microscopy (ZPC-cryoEM) is an emerging technique that is capable of producing higher image contrast than conventional cryoEM. By combining this technique with advanced image processing methods, we achieved subnanometer resolution for two biological specimens: 2D bacteriorhodopsin crystal and epsilon15 bacteriophage. For an asymmetric reconstruction of epsilon15 bacteriophage, ZPC-cryoEM can reduce the required amount of data by a factor of approximately 3, compared with conventional cryoEM. The reconstruction was carried out to 13 A resolution without the need to correct the contrast transfer function. New structural features at the portal vertex of the epsilon15 bacteriophage are revealed in this reconstruction. Using ZPC cryo-electron tomography (ZPC-cryoET), a similar level of data reduction and higher resolution structures of epsilon15 bacteriophage can be obtained relative to conventional cryoET. These results show quantitatively the benefits of ZPC-cryoEM and ZPC-cryoET for structural determinations of macromolecular machines at nanometer and subnanometer resolutions.
History
DepositionJun 30, 2010-
Header (metadata) releaseSep 1, 2010-
Map releaseSep 1, 2010-
UpdateJul 8, 2011-
Current statusJul 8, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5203_1.png

Downloads & links

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Map

FileDownload / File: emd_5203.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered top-view of epsilon 15 phage reconstructed with 50 subtomograms taken with a Zernike phase plate.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.88 Å/pix.
x 216 pix.
= 1054.08 Å		4.88 Å/pix.
x 216 pix.
= 1054.08 Å		4.88 Å/pix.
x 216 pix.
= 1054.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-2.5528 - 7.42697
Average (Standard dev.)0.1067 (±0.540465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 1054.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.884.884.88
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z1054.0801054.0801054.080
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/NS216216216
D min/max/mean-2.5537.4270.107

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Supplemental data

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Sample components

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Entire : Epsilon 15

EntireName: Epsilon 15
Components
  • Sample: Epsilon 15
  • Virus: epsilon15 (virus)

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Supramolecule #1000: Epsilon 15

SupramoleculeName: Epsilon 15 / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1

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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 (bacteria) / synonym: BACTERIA(EUBACTERIA)
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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureAverage: 90 K
Specialist opticsEnergy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Image recordingNumber real images: 71 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.3 mm / Nominal magnification: 20000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °

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Image processing

DetailsAverage number of projections used in the 3D reconstructions: 50.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF

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