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- EMDB-18071: 48-nm repeat of the native axonemal doublet microtubule from bovi... -

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Entry
Database: EMDB / ID: EMD-18071
Title48-nm repeat of the native axonemal doublet microtubule from bovine sperm, local refinement A-lumen top
Map datadeepEMhancer map (unmasked)
Sample
  • Complex: 48-nm repeat of the native axonemal doublet microtubule from bovine sperm
Keywordsmicrotubule / cilia / sperm / axoneme / STRUCTURAL PROTEIN
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLeung MR / Zeng J / Zhang R / Zeev-Ben-Mordehai T
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)740.018.007 Netherlands
CitationJournal: Cell / Year: 2023
Title: Structural specializations of the sperm tail.
Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai /
Abstract: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level.
History
DepositionAug 2, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18071.png

Downloads & links

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Map

FileDownload / File: emd_18071.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer map (unmasked)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 672 pix.
= 699.552 Å		1.04 Å/pix.
x 672 pix.
= 699.552 Å		1.04 Å/pix.
x 672 pix.
= 699.552 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.052707706 - 2.2539012
Average (Standard dev.)0.0067747403 (±0.048132256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 699.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18071_msk_1.map
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Additional map: unsharpened map

Fileemd_18071_additional_1.map
Annotationunsharpened map
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Additional map: deepEMhancer map (masked)

Fileemd_18071_additional_2.map
AnnotationdeepEMhancer map (masked)
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Half map: half-map 1

Fileemd_18071_half_map_1.map
Annotationhalf-map 1
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Half map: half-map 2

Fileemd_18071_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : 48-nm repeat of the native axonemal doublet microtubule from bovi...

EntireName: 48-nm repeat of the native axonemal doublet microtubule from bovine sperm
Components
  • Complex: 48-nm repeat of the native axonemal doublet microtubule from bovine sperm

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Supramolecule #1: 48-nm repeat of the native axonemal doublet microtubule from bovi...

SupramoleculeName: 48-nm repeat of the native axonemal doublet microtubule from bovine sperm
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#66
Source (natural)Organism: Bos taurus (cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 532665
Startup modelType of model: EMDB MAP
EMDB ID:

24664

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 34083
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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