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- EMDB-40621: cryo-EM density map of the 48-nm repeat doublet microtubule witho... -

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Basic information

Entry
Database: EMDB / ID: EMD-40621
Titlecryo-EM density map of the 48-nm repeat doublet microtubule without beak from Chlamydomonas
Map data
Sample
  • Complex: Chlamydomonas DMTs
KeywordsChlamydomonas / Tektin / beak / doublet microtubule / DMT / microtubule inner protein / cilia / flagella / FAP / CFAP / MIP / MAP / cytoskeleton / tublin / STRUCTURAL PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZeng J / Zhang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 United States
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
DepositionApr 26, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40621.png

Downloads & links

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Map

FileDownload / File: emd_40621.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 512 pix.
= 711.68 Å		1.39 Å/pix.
x 512 pix.
= 711.68 Å		1.39 Å/pix.
x 512 pix.
= 711.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum0.0 - 2.0822644
Average (Standard dev.)0.011537011 (±0.07638465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 711.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40621_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_40621_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_40621_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_40621_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chlamydomonas DMTs

EntireName: Chlamydomonas DMTs
Components
  • Complex: Chlamydomonas DMTs

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Supramolecule #1: Chlamydomonas DMTs

SupramoleculeName: Chlamydomonas DMTs / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 39.6 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

20631

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 222476
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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