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- EMDB-1697: Outer dynein arms with a microtubule doublet in the presence of A... -

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Basic information

Entry
Database: EMDB / ID: EMD-1697
TitleOuter dynein arms with a microtubule doublet in the presence of ADP.Vanadate
Map dataThis is an image of outer dynein arms with a microtubule doublet in the presence of ADP.Vanadate
Sample
  • Sample: Outer dynein arm, microtubule doublet
  • Organelle or cellular component: FlagellaFlagellum
KeywordsDynein / flagella / ATP / tomography / motility / tubulin / microtubule
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 39.0 Å
AuthorsMovassagh T / Bui KH / Sakakibara H / Oiwa K / Ishikawa T
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis.
Authors: Tandis Movassagh / Khanh Huy Bui / Hitoshi Sakakibara / Kazuhiro Oiwa / Takashi Ishikawa /
Abstract: Outer and inner dynein arms generate force for the flagellar/ciliary bending motion. Although nucleotide-induced structural change of dynein heavy chains (the ATP-driven motor) was proven in vitro, ...Outer and inner dynein arms generate force for the flagellar/ciliary bending motion. Although nucleotide-induced structural change of dynein heavy chains (the ATP-driven motor) was proven in vitro, our lack of knowledge in situ has precluded an understanding of the bending mechanism. Here we reveal nucleotide-induced global structural changes of the outer and inner dynein arms of Chlamydomonas reinhardtii flagella in situ using electron cryotomography. The ATPase domains of the dynein heavy chains move toward the distal end, and the N-terminal tail bends sharply during product release. This motion could drive the adjacent microtubule to cause a sliding motion. In contrast to in vitro results, in the presence of nucleotides, outer dynein arms coexist as clusters of apo or nucleotide-bound forms in situ. This implies a cooperative switching, which may be related to the mechanism of bending.
History
DepositionJan 26, 2010-
Header (metadata) releaseMay 13, 2010-
Map releaseMay 13, 2010-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1697.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of outer dynein arms with a microtubule doublet in the presence of ADP.Vanadate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.85 Å/pix.
x 54 pix.
= 369.9 Å
6.85 Å/pix.
x 128 pix.
= 808.3 Å
6.85 Å/pix.
x 118 pix.
= 876.8 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: 6.85 Å
Density
Contour LevelBy AUTHOR: 0.0
Minimum - Maximum-5.70157 - 9.42592
Average (Standard dev.)0.246369 (±1.69908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions12811854
Spacing12811854
CellA: 876.8 Å / B: 808.3 Å / C: 369.9 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.856.856.85
M x/y/z12811854
origin x/y/z0.0000.0000.000
length x/y/z876.800808.300369.900
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS11812854
D min/max/mean-5.7029.4260.246

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Supplemental data

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Sample components

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Entire : Outer dynein arm, microtubule doublet

EntireName: Outer dynein arm, microtubule doublet
Components
  • Sample: Outer dynein arm, microtubule doublet
  • Organelle or cellular component: FlagellaFlagellum

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Supramolecule #1000: Outer dynein arm, microtubule doublet

SupramoleculeName: Outer dynein arm, microtubule doublet / type: sample / ID: 1000 / Details: The sample was flagella in situ / Number unique components: 1

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Supramolecule #1: Flagella

SupramoleculeName: Flagella / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Outer dynein arm and Microtubule doublet / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / synonym: Green Algae / Organelle: Flagella / Location in cell: Axoneme

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 30 mM HEPES (pH 7.4), 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, 50 mM Potassium Acetate, 0.5% (w/v) Polyethylene Glycol (MW 20,000), 0.1 mM ATP with 0.05 mM sodium Orthovanadate
GridDetails: 300 mesh lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 10.0 eV / Energy filter - Upper energy threshold: 25.0 eV
Sample stageSpecimen holder: Eucentric Gatan cryo / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
TemperatureAverage: 100 K
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 6.85 µm / Number real images: 1200 / Average electron dose: 30 e/Å2 / Bits/pixel: 16

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD
DetailsAverage number of projections used in the 3D reconstructions: 6097. Average number of class averages: 2.

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