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- EMDB-6524: Structure and function of outer dynein intermediate and light cha... -

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Basic information

Entry
Database: EMDB / ID: EMD-6524
TitleStructure and function of outer dynein intermediate and light chain complex
Map dataStreptavidin-labeled LC10CBCCP axoneme
Sample
  • Sample: Streptavidin-labeled LC10CBCCP axoneme
  • Organelle or cellular component: axoneme
Keywordscilia and flagella / axoneme / outer dynein arm / intermediate chain / light chain
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 47.0 Å
AuthorsOda T / Abe T / Yanagisawa H / Kikkawa M
CitationJournal: Mol Biol Cell / Year: 2016
Title: Structure and function of outer dynein arm intermediate and light chain complex.
Authors: Toshiyuki Oda / Tatsuki Abe / Haruaki Yanagisawa / Masahide Kikkawa /
Abstract: The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). ...The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). Although the three-dimensional (3D) structure of the whole ODA complex has been investigated, the 3D configurations of the ICs and LCs are largely unknown. Here we identified the 3D positions of the two ICs and three LCs using cryo-electron tomography and structural labeling. We found that these ICs and LCs were all localized at the root of the outer-inner dynein (OID) linker, designated the ODA-Beak complex. Of interest, the coiled-coil domain of IC2 extended from the ODA-Beak to the outer surface of ODA. Furthermore, we investigated the molecular mechanisms of how the OID linker transmits signals to the ODA-Beak, by manipulating the interaction within the OID linker using a chemically induced dimerization system. We showed that the cross-linking of the OID linker strongly suppresses flagellar motility in vivo. These results suggest that the ICs and LCs of the ODA form the ODA-Beak, which may be involved in mechanosignaling from the OID linker to the HCs.
History
DepositionNov 15, 2015-
Header (metadata) releaseDec 9, 2015-
Map releaseFeb 24, 2016-
UpdateFeb 24, 2016-
Current statusFeb 24, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 275
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 275
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6524.gif

Downloads & links

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Map

FileDownload / File: emd_6524.map.gz / Format: CCP4 / Size: 19 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStreptavidin-labeled LC10CBCCP axoneme
Voxel sizeX=Y=Z: 6.07 Å
Density
Contour LevelBy AUTHOR: 275.0 / Movie #1: 275
Minimum - Maximum0.0 - 535.444335939999974
Average (Standard dev.)133.621780400000006 (±131.755996699999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200150170
Spacing200150170
CellA: 910.5 Å / B: 1214.0 Å / C: 1031.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.076.076.07
M x/y/z150200170
origin x/y/z0.0000.0000.000
length x/y/z910.5001214.0001031.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150200170
D min/max/mean0.000535.444133.622

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Supplemental data

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Sample components

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Entire : Streptavidin-labeled LC10CBCCP axoneme

EntireName: Streptavidin-labeled LC10CBCCP axoneme
Components
  • Sample: Streptavidin-labeled LC10CBCCP axoneme
  • Organelle or cellular component: axoneme

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Supramolecule #1000: Streptavidin-labeled LC10CBCCP axoneme

SupramoleculeName: Streptavidin-labeled LC10CBCCP 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 25700
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DateSep 5, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 100 e/Å2

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET / Number subtomograms used: 948
DetailsNumber of tilts (projections) used in 3D reconstruction: 60 Tomographic tilt angle increment: 2

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