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- EMDB-46492: The cryo-EM structure of RS3 (base and stalk) of mouse respirator... -

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Basic information

Entry
Database: EMDB / ID: EMD-46492
TitleThe cryo-EM structure of RS3 (base and stalk) of mouse respiratory cilia
Map datastructure of RS3 (base and stalk) of mouse respiratory cilia
Sample
  • Organelle or cellular component: RS3 from mouse respiratory cilia
Keywordsaxoneme / radial spoke / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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: To Be Published
Title: The cryo-EM structure of mouse radial spoke 3 reveals a unique metabolic and regulatory hub in cilia
Authors: Yanhe Z / Xuewu Z / Daniela N
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46492.png

Downloads & links

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Map

FileDownload / File: emd_46492.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of RS3 (base and stalk) of mouse respiratory cilia
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 360 pix.
= 776.88 Å		2.16 Å/pix.
x 360 pix.
= 776.88 Å		2.16 Å/pix.
x 360 pix.
= 776.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.158 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.023860846 - 0.037276514
Average (Standard dev.)0.000014112508 (±0.0004438041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 776.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_46492_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46492_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RS3 from mouse respiratory cilia

EntireName: RS3 from mouse respiratory cilia
Components
  • Organelle or cellular component: RS3 from mouse respiratory cilia

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Supramolecule #1: RS3 from mouse respiratory cilia

SupramoleculeName: RS3 from mouse respiratory cilia / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#29
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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 R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE
Details: 4 microliters of splayed axoneme sample were applied to glow-discharged Quantifoil R2/2 Cu grids. After removing excess liquid by blotting the grid from the backside with Whatman filter ...Details: 4 microliters of splayed axoneme sample were applied to glow-discharged Quantifoil R2/2 Cu grids. After removing excess liquid by blotting the grid from the backside with Whatman filter paper for 2-3 s, the grid was immediately plunge-frozen in liquid ethane using a home-made plunge freezer..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 50000 / Average exposure time: 4.2 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 280000
Details: particles containing RS3 were manually picked (using the conserved spacing of RSs as guide) centering on the A-tubule of the DMT
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: For the RS3 head, neck, and stalk, the AlphaFold2 models of mouse were used.
Details: For the RS3 base, the PDB entry 8J07 was used as starting.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 63152
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final 3D classificationSoftware - Name: RELION (ver. 5)

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