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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: 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_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)

Slices (2/3)

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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