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- EMDB-7488: The tether and tether head complex and I1 dynein complex region e... -

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Basic information

Entry
Database: EMDB / ID: 7488
TitleThe tether and tether head complex and I1 dynein complex region extracted from the cryo-electron tomography and subtomographic average (1622 axonemal repeats) of isolated Tetrahymena wild type cilia
Map dataThe tether and tether head complex and I1 dynein complex region extracted from the cryo-electron tomography and subtomographic average (1622 axonemal repeats) of isolated Tetrahymena wild type cilia
SampleThe tether and tether head complex and I1 dynein complex region extracted from the cryo-electron tomography and subtomographic average (1622 axonemal repeats) of isolated Tetrahymena wild type cilia:
SourceTetrahymena thermophila (eukaryote)
Methodelectron tomography / cryo EM / 33 Å resolution
AuthorsFu G / Wang Q / Phan N / Urbanska P / Joachimiak E / Lin J / Wloga D / Nicastro D
CitationJournal: Mol. Biol. Cell / Year: 2018
Title: The I1 dynein-associated tether and tether head complex is a conserved regulator of ciliary motility.
Authors: Gang Fu / Qian Wang / Nhan Phan / Paulina Urbanska / Ewa Joachimiak / Jianfeng Lin / Dorota Wloga / Daniela Nicastro
DateDeposition: Mar 1, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Mar 21, 2018 / Last update: Jun 6, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 126
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 126
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7488.map.gz (map file in CCP4 format, 529 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
55 pix
10 Å/pix.
= 549.835 Å
40 pix
10 Å/pix.
= 399.88 Å
60 pix
10 Å/pix.
= 599.82 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.997 Å
Density
Contour Level:126 (by author), 126 (movie #1):
Minimum - Maximum83.131743999999998 - 182.803629999999998
Average (Standard dev.)125.717209999999994 (11.817368500000001)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions406055
Origin-30-39-32
Limit92022
Spacing604055
CellA: 599.82 Å / B: 399.88 Å / C: 549.83496 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.9979.9979.997
M x/y/z604055
origin x/y/z0.0000.0000.000
length x/y/z599.820399.880549.835
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-39-30-32
NC/NR/NS604055
D min/max/mean83.132182.804125.717

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Supplemental data

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Sample components

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Entire The tether and tether head complex and I1 dynein complex region e...

EntireName: The tether and tether head complex and I1 dynein complex region extracted from the cryo-electron tomography and subtomographic average (1622 axonemal repeats) of isolated Tetrahymena wild type cilia
Number of components: 1

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Component #1: cellular-component, The tether and tether head complex and I1 dyn...

Cellular-componentName: The tether and tether head complex and I1 dynein complex region extracted from the cryo-electron tomography and subtomographic average (1622 axonemal repeats) of isolated Tetrahymena wild type cilia
Recombinant expression: No
SourceSpecies: Tetrahymena thermophila (eukaryote) / Strain: wild type

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Experimental details

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Sample preparation

SpecimenSpecimen state: tissue / Method: cryo EM
Sample solutionBuffer solution: Solutions were freshly made before use. / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 1 K
Details: back-side blotting for 1.5-2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 13500 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 6000.0 - 8000.0 nm / Energy filter: GIF 2000 / Energy window: 0-20 eV
Specimen HolderModel: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 2 deg. / Number of sections: 720
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD / Resolution: 33 Å / Resolution method: FSC 0.5 CUT-OFF

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