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- EMDB-2633: Outer arm dynein dimer from mouse respiratory cilia in pre-power ... -

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Basic information

Entry
Database: EMDB / ID: EMD-2633
TitleOuter arm dynein dimer from mouse respiratory cilia in pre-power stroke (SH-P)
Map datasubtomogram averaging of dynein dimers from mouse respiratory cilia in the SH-P form (pre-power stroke)
Sample
  • Sample: dynein dimer in the SH-P form (pre-power stroke)
  • Organelle or cellular component: Cilia
Keywordsdynein / ATP / cilia / cryo-electron tomography
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsUeno H / Bui KH / Ishikawa T / Imai Y / Yamaguchi T
CitationJournal: Cytoskeleton (Hoboken) / Year: 2014
Title: Structure of dimeric axonemal dynein in cilia suggests an alternative mechanism of force generation.
Authors: Hironori Ueno / Khanh Huy Bui / Takuji Ishikawa / Yohsuke Imai / Takami Yamaguchi / Takashi Ishikawa /
Abstract: The mechanism by which the two different heads of the ciliary outer dynein arm produce force to translocate the microtubule during beating is still unknown. In this report we use cryo-electron ...The mechanism by which the two different heads of the ciliary outer dynein arm produce force to translocate the microtubule during beating is still unknown. In this report we use cryo-electron tomography and image processing to analyze the conformational changes and the relative abundance of each conformation of the two dynein heads from mouse respiratory cilia. In the absence of nucleotides the majority of dynein dimers are in the apo form and both heads are tightly packed, whereas they are dissociated and move independently in the presence of nucleotides. The head of the external outer arm dynein heavy chain has a diagonal shift toward both the neighboring B-tubule and the proximal end of the axoneme, while the head of the internal heavy chain shifts only longitudinally toward the proximal end. In the presence of nucleotides a significant number of the dynein dimers have two heads overlapped in the proximal shifting form or overlapped in the apo form. During ciliary bending axonemal dynein translocates microtubules by moving with short steps and two heads stay at the same position longer than cytoplasmic dynein. This demonstrates that the step of the outer arm dynein dimer is not dominated by the hand-over-hand motion, but also indicates the difference between axonemal dynein and cytoplasmic dynein.
History
DepositionApr 23, 2014-
Header (metadata) releaseMay 14, 2014-
Map releaseJul 2, 2014-
UpdateAug 27, 2014-
Current statusAug 27, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2633.tif

Downloads & links

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Map

FileDownload / File: emd_2633.map.gz / Format: CCP4 / Size: 11.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram averaging of dynein dimers from mouse respiratory cilia in the SH-P form (pre-power stroke)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.25 Å/pix.
x 80 pix.
= 580. Å		7.25 Å/pix.
x 200 pix.
= 1450. Å		7.25 Å/pix.
x 200 pix.
= 1450. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-6.66773272 - 10.13240242
Average (Standard dev.)0.0087037 (±1.07533503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-70
Dimensions20020080
Spacing20020080
CellA: 1450.0 Å / B: 1450.0 Å / C: 580.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.257.257.25
M x/y/z20020080
origin x/y/z0.0000.0000.000
length x/y/z1450.0001450.000580.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS00-70
NC/NR/NS20020080
D min/max/mean-6.66810.1320.009

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Supplemental data

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Sample components

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Entire : dynein dimer in the SH-P form (pre-power stroke)

EntireName: dynein dimer in the SH-P form (pre-power stroke)
Components
  • Sample: dynein dimer in the SH-P form (pre-power stroke)
  • Organelle or cellular component: Cilia

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Supramolecule #1000: dynein dimer in the SH-P form (pre-power stroke)

SupramoleculeName: dynein dimer in the SH-P form (pre-power stroke) / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Cilia

SupramoleculeName: Cilia / type: organelle_or_cellular_component / ID: 1 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57Bl/6 / synonym: house mouse / Tissue: trachea / Cell: epidermal / Organelle: cilia

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

GridDetails: Quantifoil holey grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 100 K / Average: 95 K
Specialist opticsEnergy filter - Name: GIF Tridiem / Energy filter - Lower energy threshold: 20.0 eV / Energy filter - Upper energy threshold: 25.0 eV
DateDec 14, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 40 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 19303 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.5 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: IMOD / Number subtomograms used: 61

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Atomic model buiding 1

Initial modelPDB ID:

3vkg

SoftwareName: Chimera
DetailsAAA domains, stalk, and buttress are considered as a rigid body. Only the linker was flexibly fitted.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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