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- EMDB-9040: Analysis of bacteriophage phiX174 tomograms using the locked self... -

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Basic information

Entry
Database: EMDB / ID: EMD-9040
TitleAnalysis of bacteriophage phiX174 tomograms using the locked self-rotation function
Map dataThe map was calculated by averaging of ten icosahedrally-averaged maps of individual phiX174 particles.
Sample
  • Virus: Enterobacteria phage phiX174 (virus)
Biological speciesEnterobacteria phage phiX174 (virus)
Methodelectron tomography / cryo EM
AuthorsFokine A / Sun Y / Khare B / Rossmann MG
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)M CB - 1515260 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076331 United States
CitationJournal: J Struct Biol / Year: 2019
Title: Enhancement of tomogram interpretability using the locked self-rotation function.
Authors: Andrei Fokine / Baldeep Khare / Yingyuan Sun / Michael G Rossmann /
Abstract: The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the ...The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability. Sub-tomograms of the icosahedral bacteriophage phiX174 are used to demonstrate the procedure.
History
DepositionAug 13, 2018-
Header (metadata) releaseSep 19, 2018-
Map releaseFeb 27, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing 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
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9040.png

Downloads & links

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Map

FileDownload / File: emd_9040.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map was calculated by averaging of ten icosahedrally-averaged maps of individual phiX174 particles.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.2 Å/pix.
x 80 pix.
= 416. Å		5.2 Å/pix.
x 80 pix.
= 416. Å		5.2 Å/pix.
x 80 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 1
Minimum - Maximum-30.059168 - 38.214554
Average (Standard dev.)0.0000000704 (±9.404064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin555
Dimensions808080
Spacing808080
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS555
NC/NR/NS808080
D min/max/mean-30.05938.2150.000

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Supplemental data

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_1.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_10.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The map was produced by averaging of eight...

Fileemd_9040_additional_11.map
AnnotationThe map was produced by averaging of eight maps of individual phiX174 particles calculated using the D5 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_2.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_3.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_4.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_5.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_6.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_7.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_8.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Tomogram of one bacteriophage phiX174 particle.

Fileemd_9040_additional_9.map
AnnotationTomogram of one bacteriophage phiX174 particle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage phiX174

EntireName: Enterobacteria phage phiX174 (virus)
Components
  • Virus: Enterobacteria phage phiX174 (virus)

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Supramolecule #1: Enterobacteria phage phiX174

SupramoleculeName: Enterobacteria phage phiX174 / type: virus / ID: 1 / Parent: 0 / Details: The virus was grown in E.coli cells. / NCBI-ID: 10847 / Sci species name: Enterobacteria phage phiX174 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / Diameter: 320.0 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormula
0.05 MNH4Cl4
0.05 MNaCl
0.1 MKCl
0.1 MTris-HCl
0.001 MMgSO4
0.005 MEDTA
GridModel: C-flat-2/2 4C / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3
DetailsThe concentration of the virus was 10**12 pfu/ml
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion, Wageningen, Netherland / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.73 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 3.0 µm / Nominal magnification: 11000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41

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