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- EMDB-20683: Average of the mid basal body from bovine respiratory cilia -

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Basic information

Entry
Database: EMDB / ID: EMD-20683
TitleAverage of the mid basal body from bovine respiratory cilia
Map data
SampleNascent axoneme from bovine respiratory epithelial cells
Biological speciesBos taurus (cattle)
Methodsubtomogram averaging / cryo EM / Resolution: 33.2 Å
AuthorsGreenan GA / Vale RD / Agard DA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM118099 United States
National Institutes of Health/National Institute of General Medical SciencesGM118106 United States
CitationJournal: To Be Published
Title: Defining the transition zone in motile cilia using electron cryo-tomography
Authors: Greenan GA / Vale RD / Agard DA
History
DepositionSep 4, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseDec 4, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20683.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.18 Å/pix.
x 150 pix.
= 1227. Å
8.18 Å/pix.
x 150 pix.
= 1227. Å
8.18 Å/pix.
x 150 pix.
= 1227. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.18 Å
Density
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-12.665031 - 17.018778
Average (Standard dev.)0.018780975 (±0.82400346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 1227.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.188.188.18
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z1227.0001227.0001227.000
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-12.66517.0190.019

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Supplemental data

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Sample components

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Entire Nascent axoneme from bovine respiratory epithelial cells

EntireName: Nascent axoneme from bovine respiratory epithelial cells
Number of components: 1

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Component #1: cellular-component, Nascent axoneme from bovine respiratory epith...

Cellular-componentName: Nascent axoneme from bovine respiratory epithelial cells
Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (natural)Organelle: cilium

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 % / Details: 15 second blot.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 1386
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 33.2 Å / Resolution method: FSC 0.143 CUT-OFF

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