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- EMDB-5206: Epsilon15 icosahedral reconstruction using Zernike phase contrast... -

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Basic information

Entry
Database: EMDB / ID: EMD-5206
TitleEpsilon15 icosahedral reconstruction using Zernike phase contrast electron microscopy
Map dataepsilon15 icosahedral capsid density map reconstructed from ZPC-cryoEM images
Sample
  • Sample: Epsilon 15Salmonella virus Epsilon15
  • Virus: epsilon15 (virus)
KeywordsPhase contrast / cryoEM / electron microscopy / bacteriophage / epsilon15
Biological speciesepsilon15 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 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
DepositionJul 1, 2010-
Header (metadata) releaseJul 19, 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: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5206_1.png

Downloads & links

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Map

FileDownload / File: emd_5206.map.gz / Format: CCP4 / Size: 339.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationepsilon15 icosahedral capsid density map reconstructed from ZPC-cryoEM images
Voxel sizeX=Y=Z: 1.95 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.66684 - 1.75931
Average (Standard dev.)0.102424 (±0.304026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-225-225-225
Dimensions450450450
Spacing450450450
CellA=B=C: 877.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.951.951.95
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z877.500877.500877.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS450450450
D min/max/mean-1.6671.7590.102

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Supplemental data

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Sample components

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Entire : Epsilon 15

EntireName: Epsilon 15Salmonella virus Epsilon15
Components
  • Sample: Epsilon 15Salmonella virus Epsilon15
  • 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.3 mm / Nominal magnification: 75000
Specialist opticsEnergy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 90 K
DateDec 1, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Number real images: 431 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: no CTF correction
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA
Details: There is no ctf correction in the final reconstruction, but we used cross common line correlation algorithm to threw away some large defocus particles whose first ctf-zeros fall within 10A.
Number images used: 2900
DetailsThe particles were selected using the consistency criterion of MPSA

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