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- EMDB-64223: 96-nm repeating structure of the axonemal doublets form mouse sperm -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64223
Title96-nm repeating structure of the axonemal doublets form mouse sperm
Map data
Sample
  • Cell: Central appratus of mouse sperm
Keywordsaxoneme / CYTOSOLIC PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 32.1 Å
AuthorsRen JQ / Zhao LY / Feng W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-Electron Tomography Elucidates the Role of KIF9 in Mammalian Sperm Axoneme Organization and Function
Authors: Zhao LY / Ren JQ
History
DepositionApr 17, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64223.png

Downloads & links

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Map

FileDownload / File: emd_64223.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 384 pix.
= 1305.6 Å		3.4 Å/pix.
x 384 pix.
= 1305.6 Å		3.4 Å/pix.
x 384 pix.
= 1305.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-12.704329 - 13.405874000000001
Average (Standard dev.)0.036766943 (±1.0000587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 1305.6001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64223_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64223_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 : Central appratus of mouse sperm

EntireName: Central appratus of mouse sperm
Components
  • Cell: Central appratus of mouse sperm

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Supramolecule #1: Central appratus of mouse sperm

SupramoleculeName: Central appratus of mouse sperm / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
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
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
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: 32.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 6
ExtractionNumber tomograms: 6 / Number images used: 2279 / Software - Name: EMAN2
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: EMAN2
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN2
FSC plot (resolution estimation)

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