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- EMDB-12119: Cropped map of the wild type Tetrahymena axoneme 96nm-repeat, obt... -

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Basic information

Entry
Database: EMDB / ID: EMD-12119
TitleCropped map of the wild type Tetrahymena axoneme 96nm-repeat, obtained by cryo-ET and subtomogram averaging, with the structures of the next-dynein regulatory complex (N-DRC) and of the Ccdc96/Ccdc113 complex.
Map dataCropped map of the Tetrahymena axoneme 96nm-repeat, by cryo-ET and subtomogram averaging, with the structures of the next-dynein regulatory complex (N-DRC) and of the Ccdc96/Ccdc113 complex.
Sample
  • Organelle or cellular component: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
Biological speciesTetrahymena thermophila CU428 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsBazan R / Schrofel A / Joachimiak E / Poprzeczko M / Pigino G / Wloga D
Funding support Germany, Poland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)819826 Germany
H2020 Marie Curie Actions of the European Commission753954 Germany
Polish National Science Centre2014/14/M/NZ3/00511 Poland
Polish National Science CentreNo 2016/23/N/NZ3/02420 Poland
CitationJournal: PLoS Genet / Year: 2021
Title: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
Authors: Rafał Bazan / Adam Schröfel / Ewa Joachimiak / Martyna Poprzeczko / Gaia Pigino / Dorota Wloga /
Abstract: Ciliary beating requires the coordinated activity of numerous axonemal complexes. The protein composition and role of radial spokes (RS), nexin links (N-DRC) and dyneins (ODAs and IDAs) is well ...Ciliary beating requires the coordinated activity of numerous axonemal complexes. The protein composition and role of radial spokes (RS), nexin links (N-DRC) and dyneins (ODAs and IDAs) is well established. However, how information is transmitted from the central apparatus to the RS and across other ciliary structures remains unclear. Here, we identify a complex comprising the evolutionarily conserved proteins Ccdc96 and Ccdc113, positioned parallel to N-DRC and forming a connection between RS3, dynein g, and N-DRC. Although Ccdc96 and Ccdc113 can be transported to cilia independently, their stable docking and function requires the presence of both proteins. Deletion of either CCDC113 or CCDC96 alters cilia beating frequency, amplitude and waveform. We propose that the Ccdc113/Ccdc96 complex transmits signals from RS3 and N-DRC to dynein g and thus regulates its activity and the ciliary beat pattern.
History
DepositionDec 15, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 118
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 118
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12119.png

Downloads & links

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Map

FileDownload / File: emd_12119.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCropped map of the Tetrahymena axoneme 96nm-repeat, by cryo-ET and subtomogram averaging, with the structures of the next-dynein regulatory complex (N-DRC) and of the Ccdc96/Ccdc113 complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7 Å/pix.
x 55 pix.
= 385. Å		7 Å/pix.
x 80 pix.
= 560. Å		7 Å/pix.
x 77 pix.
= 539. 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 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 118.0 / Movie #1: 118
Minimum - Maximum8.4914055 - 225.4574
Average (Standard dev.)107.73215 (±29.114592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin030
Dimensions807755
Spacing778055
CellA: 539.0 Å / B: 560.0 Å / C: 385.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z777
M x/y/z778055
origin x/y/z0.0000.0000.000
length x/y/z539.000560.000385.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS300
NC/NR/NS778055
D min/max/mean8.491225.457107.732

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Supplemental data

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Sample components

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Entire : Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that...

EntireName: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
Components
  • Organelle or cellular component: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.

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Supramolecule #1: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that...

SupramoleculeName: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila CU428 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1600
ExtractionNumber tomograms: 14 / Number images used: 1600
Final angle assignmentType: NOT APPLICABLE

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