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- EMDB-6504: Docking complex-independent alignment of outer dynein arms with 2... -

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Basic information

Entry
Database: EMDB / ID: EMD-6504
TitleDocking complex-independent alignment of outer dynein arms with 24-nm periodicity
Map dataStreptavidin-labeled DC1-M71BCCP axoneme
Sample
  • Sample: Streptavidin-labeled ODA structure from DC1-M71BCCP axoneme
  • Organelle or cellular component: axoneme
Keywordscilia and flagella / axoneme / outer dynein arm / docking complex
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 47.0 Å
AuthorsOda T / Abe T / Yanagisawa H / Kikkawa M
CitationJournal: J Cell Sci / Year: 2016
Title: Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro.
Authors: Toshiyuki Oda / Tatsuki Abe / Haruaki Yanagisawa / Masahide Kikkawa /
Abstract: The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to ...The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complexin vitro Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler.
History
DepositionNov 12, 2015-
Header (metadata) releaseNov 25, 2015-
Map releaseMar 16, 2016-
UpdateMar 16, 2016-
Current statusMar 16, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 34.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 34.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6504.gif

Downloads & links

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Map

FileDownload / File: emd_6504.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStreptavidin-labeled DC1-M71BCCP axoneme
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.07 Å/pix.
x 70 pix.
= 424.9 Å		6.07 Å/pix.
x 70 pix.
= 424.9 Å		6.07 Å/pix.
x 70 pix.
= 424.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 34.200000000000003 / Movie #1: 34.2
Minimum - Maximum-174.488677980000006 - 265.831115720000014
Average (Standard dev.)16.356616970000001 (±69.443717960000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions707070
Spacing707070
CellA=B=C: 424.90002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.076.076.07
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z424.900424.900424.900
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-174.489265.83116.357

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Supplemental data

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Sample components

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Entire : Streptavidin-labeled ODA structure from DC1-M71BCCP axoneme

EntireName: Streptavidin-labeled ODA structure from DC1-M71BCCP axoneme
Components
  • Sample: Streptavidin-labeled ODA structure from DC1-M71BCCP axoneme
  • Organelle or cellular component: axoneme

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Supramolecule #1000: Streptavidin-labeled ODA structure from DC1-M71BCCP axoneme

SupramoleculeName: Streptavidin-labeled ODA structure from DC1-M71BCCP axoneme
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: axoneme

SupramoleculeName: axoneme / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: flagella

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.2
Details: 30 mM Hepes-NaOH pH 7.2, 5 mM MgCl2, 1 mM dithiothreitol, 1 mM EGTA, 50 mM K-acetate
GridDetails: 300 mesh copper grid, holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 5 seconds before plunging

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Electron microscopy

MicroscopeOTHER
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateFeb 2, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 25700
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

DetailsNumber of tilts (projections) used in 3D reconstruction: 60 Tomographic tilt angle increment: 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET / Number subtomograms used: 784

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