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- EMDB-61221: In situ structure of radial spoke 1 base in the axoneme of mouse sperm -

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Basic information

Entry
Database: EMDB / ID: EMD-61221
TitleIn situ structure of radial spoke 1 base in the axoneme of mouse sperm
Map data
Sample
  • Cell: mouse sperm
Keywordsmicrotubules / axoneme / sperm / filament / PROTEIN TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 13.51 Å
AuthorsZhu Y / Yin GL / Sun F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925026 China
CitationJournal: To Be Published
Title: In-cell architecture of axonemal radial spokes in mouse sperm
Authors: Zhu Y / Yin GL / Sun F
History
DepositionAug 20, 2024-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61221.png

Downloads & links

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Map

FileDownload / File: emd_61221.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00545
Minimum - Maximum-0.009253446 - 0.017165078
Average (Standard dev.)0.000005799548 (±0.0015877958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61221_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61221_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61221_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse sperm

EntireName: mouse sperm
Components
  • Cell: mouse sperm

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Supramolecule #1: mouse sperm

SupramoleculeName: mouse sperm / type: cell / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6000
ExtractionNumber tomograms: 689 / Number images used: 37018
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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