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- EMDB-46485: Cryo-electron tomography and subtomogram averaging of AK1-/- mous... -

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Basic information

Entry
Database: EMDB / ID: EMD-46485
TitleCryo-electron tomography and subtomogram averaging of AK1-/- mouse respiratory ciliary axoneme
Map dataCryo-electron tomography and subtomogram averaging of AK1-/- mouse respiratory ciliary axoneme
Sample
  • Organelle or cellular component: Respiratory ciliary axonemes from mouse
Keywordsaxoneme / radial spoke / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 44.0 Å
AuthorsYanhe Z / Xuewu Z / Daniela N
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM083122 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140082 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mouse radial spoke 3 is a metabolic and regulatory hub in cilia.
Authors: Yanhe Zhao / Kangkang Song / Amirrasoul Tavakoli / Long Gui / Angeles Fernandez-Gonzalez / Song Zhang / Petras P Dzeja / S Alex Mitsialis / Xuewu Zhang / Daniela Nicastro /
Abstract: Cilia are microtubule-based organelles that have important roles in cell sensing, signaling and motility. Recent studies have revealed the atomic structures of many multicomponent ciliary complexes, ...Cilia are microtubule-based organelles that have important roles in cell sensing, signaling and motility. Recent studies have revealed the atomic structures of many multicomponent ciliary complexes, elucidating their mechanisms of action. However, little is known about the structure, proteome and function of full-length radial spoke 3 (RS3), a conserved complex that transmits mechanochemical signals to coordinate ciliary motility. Here, we combined single-particle cryo-electron microscopy, cryo-electron tomography, proteomic analysis and computational modeling to determine the three-dimensional structure and atomic model of RS3 from mouse respiratory cilia. We reveal all RS3 components, including regulatory and metabolic enzymes such as a protein kinase A subunit, adenylate kinases (AKs) and malate dehydrogenases. Furthermore, we confirm RS3 loss in AK7-deficient mice, which exhibit motility defects. Our findings identify RS3 as an important regulatory and metabolic hub that maintains sufficient adenosine triphosphate for sustained ciliary beating, providing insights into the etiology of ciliopathies.
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46485.png

Downloads & links

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Map

FileDownload / File: emd_46485.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomography and subtomogram averaging of AK1-/- mouse respiratory ciliary axoneme
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.77 Å/pix.
x 100 pix.
= 1077. Å		10.77 Å/pix.
x 100 pix.
= 1077. Å		10.77 Å/pix.
x 120 pix.
= 1292.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 132.0
Minimum - Maximum92.155715999999998 - 167.997199999999992
Average (Standard dev.)125.324875000000006 (±6.2587414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100120100
Spacing120100100
CellA: 1292.4 Å / B: 1077.0 Å / C: 1077.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half maps are unwindowed, they need to be...

Fileemd_46485_half_map_1.map
AnnotationHalf maps are unwindowed, they need to be windowed, tapered, masked or etc. before FSC calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half maps are unwindowed, they need to be...

Fileemd_46485_half_map_2.map
AnnotationHalf maps are unwindowed, they need to be windowed, tapered, masked or etc. before FSC calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Respiratory ciliary axonemes from mouse

EntireName: Respiratory ciliary axonemes from mouse
Components
  • Organelle or cellular component: Respiratory ciliary axonemes from mouse

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Supramolecule #1: Respiratory ciliary axonemes from mouse

SupramoleculeName: Respiratory ciliary axonemes from mouse / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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
Details: 30 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 13500
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 44.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 900
ExtractionNumber tomograms: 9 / Number images used: 1205
CTF correctionType: NONE
Final angle assignmentType: OTHER / Software - Name: PEET (ver. 1.10.0)
Details: angles (and shifts) for each subvolume are assigned by maximizing normalized cross-correlation between the subvolume and the reference

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