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- EMDB-70169: Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repe... -

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Entry
Database: EMDB / ID: EMD-70169
TitleSubtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repeat in RSP3A-KO Tetrahymena thermophila
Map dataMap of RSP3A-KO
Sample
  • Complex: Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repeat in RSP3A-KO Tetrahymena thermophila
KeywordsAxoneme / 96nm repeat / Cilia / RSP3A-Ko / STRUCTURAL PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 22.26 Å
AuthorsBicka MB / Ghanaeian AG / Black CB / Joachimiak EJ / Osinka AO / Majhi SM / Konopka AK / Bulska EB / Bui HB / Wloga DW
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Cell Mol Life Sci / Year: 2025
Title: Heterogeneity of radial spoke components in Tetrahymena cilia.
Authors: Marta Bicka / Avrin Ghanaeian / Corbin Black / Ewa Joachimiak / Anna Osinka / Sumita Majhi / Anna Konopka / Ewa Bulska / Khanh Huy Bui / Dorota Wloga /
Abstract: Radial spokes, RS1, RS2, and RS3, are T-shaped, multiprotein complexes that transmit regulatory signals from the central apparatus to outer doublet complexes, including dynein arms. Radial spokes, ...Radial spokes, RS1, RS2, and RS3, are T-shaped, multiprotein complexes that transmit regulatory signals from the central apparatus to outer doublet complexes, including dynein arms. Radial spokes, especially RS3, differ in their morphology, protein composition, and RS base-docked IDAs. Spokes' defects alter cilia beating frequency, waveform, and amplitude, leading, in humans, to primary ciliary dyskinesia and male infertility. The role of the particular spokes remains unclear. Ciliate Tetrahymena thermophila has three RSP3 paralogs and two or three paralogs of some other RSPs. Using multiple complementary approaches, we demonstrated that Tetrahymena forms RS1 and RS2 subtypes, each with a core composed of various RSP3 paralogs and one type of RSP3-less RS3. We elucidated proteomes of RS1 and RS2 subtypes, RS3, and identified novel RS proteins, including enzymatic proteins involved in local regulation of ADP/ATP levels, the guanylate nucleotide pathway, and protein phosphorylation, whose presence further diversifies RSs' properties and likely functions.
History
DepositionApr 11, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70169.png

Downloads & links

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Map

FileDownload / File: emd_70169.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of RSP3A-KO
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.48 Å/pix.
x 168 pix.
= 1424.64 Å		8.48 Å/pix.
x 168 pix.
= 1424.64 Å		8.48 Å/pix.
x 168 pix.
= 1424.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.506
Minimum - Maximum-26.484214999999999 - 66.277339999999995
Average (Standard dev.)1.0436443 (±10.799238000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 1424.6399 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70169_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of RSP3A-KO

Fileemd_70169_half_map_1.map
AnnotationHalf map of RSP3A-KO
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of RSP3A-KO

Fileemd_70169_half_map_2.map
AnnotationHalf map of RSP3A-KO
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repe...

EntireName: Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repeat in RSP3A-KO Tetrahymena thermophila
Components
  • Complex: Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repeat in RSP3A-KO Tetrahymena thermophila

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Supramolecule #1: Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repe...

SupramoleculeName: Subtomogram Averaged Cryo-ET Structure of the 96-nm Axonemal Repeat in RSP3A-KO Tetrahymena thermophila
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 0.004 µm / Nominal defocus min: 0.002 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 22.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2090
ExtractionNumber tomograms: 35 / Number images used: 2090
CTF correctionType: NONE
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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