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- EMDB-41376: 96nm repeat of Doublet microtubule from Tetrahymena thermophila -

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Basic information

Entry
Database: EMDB / ID: EMD-41376
Title96nm repeat of Doublet microtubule from Tetrahymena thermophila
Map data
Sample
  • Organelle or cellular component: 96nm repeat of Doublet microtubule from Tetrahymena thermophila
Keywordsnexin-dynein regulatory complex / cilia / axoneme dynein / STRUCTURAL PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.54 Å
AuthorsGhanaeian AG / Bui KH
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2023
Title: Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism.
Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward ...Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui /
Abstract: Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein ...Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein regulatory complex (N-DRC), which links adjacent doublet microtubules and regulates and coordinates the activity of outer doublet complexes. Despite its critical role in cilia motility, the assembly and molecular basis of the regulatory mechanism are poorly understood. Here, using cryo-electron microscopy in conjunction with biochemical cross-linking and integrative modeling, we localize 12 DRC subunits in the N-DRC structure of Tetrahymena thermophila. We also find that the CCDC96/113 complex is in close contact with the DRC9/10 in the linker region. In addition, we reveal that the N-DRC is associated with a network of coiled-coil proteins that most likely mediates N-DRC regulatory activity.
History
DepositionJul 28, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41376.png

Downloads & links

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Map

FileDownload / File: emd_41376.map.gz / Format: CCP4 / Size: 396.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.74 Å/pix.
x 470 pix.
= 1287.8 Å		2.74 Å/pix.
x 470 pix.
= 1287.8 Å		2.74 Å/pix.
x 470 pix.
= 1287.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.819
Minimum - Maximum-2.3632033 - 5.18283
Average (Standard dev.)0.0022235778 (±0.28897506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions470470470
Spacing470470470
CellA=B=C: 1287.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41376_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_41376_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41376_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 96nm repeat of Doublet microtubule from Tetrahymena thermophila

EntireName: 96nm repeat of Doublet microtubule from Tetrahymena thermophila
Components
  • Organelle or cellular component: 96nm repeat of Doublet microtubule from Tetrahymena thermophila

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Supramolecule #1: 96nm repeat of Doublet microtubule from Tetrahymena thermophila

SupramoleculeName: 96nm repeat of Doublet microtubule from Tetrahymena thermophila
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8537

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.54 Å / Resolution method: OTHER / Number images used: 211502
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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