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- EMDB-15450: TAILS structure in human sperm tip singlet microtubules -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-15450
TitleTAILS structure in human sperm tip singlet microtubules
Map data
Sample
  • Organelle or cellular component: Human sperm flagellum end piece
KeywordsMicrotubule Sperm TAILS / UNKNOWN FUNCTION
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsHoog JL / Zabeo DZ
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2015-05427 Sweden
CitationJournal: Sci Rep / Year: 2018
Title: A lumenal interrupted helix in human sperm tail microtubules.
Authors: Davide Zabeo / John M Heumann / Cindi L Schwartz / Azusa Suzuki-Shinjo / Garry Morgan / Per O Widlund / Johanna L Höög /
Abstract: Eukaryotic flagella are complex cellular extensions involved in many human diseases gathered under the term ciliopathies. Currently, detailed insights on flagellar structure come mostly from studies ...Eukaryotic flagella are complex cellular extensions involved in many human diseases gathered under the term ciliopathies. Currently, detailed insights on flagellar structure come mostly from studies on protists. Here, cryo-electron tomography (cryo-ET) was performed on intact human spermatozoon tails and showed a variable number of microtubules in the singlet region (inside the end-piece). Inside the microtubule plus end, a novel left-handed interrupted helix which extends several micrometers was discovered. This structure was named Tail Axoneme Intra-Lumenal Spiral (TAILS) and binds directly to 11 protofilaments on the internal microtubule wall, in a coaxial fashion with the surrounding microtubule lattice. It leaves a gap over the microtubule seam, which was directly visualized in both singlet and doublet microtubules. We speculate that TAILS may stabilize microtubules, enable rapid swimming or play a role in controlling the swimming direction of spermatozoa.
History
DepositionJul 22, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15450.png

Downloads & links

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Map

FileDownload / File: emd_15450.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.7 Å/pix.
x 60 pix.
= 462. Å		7.7 Å/pix.
x 60 pix.
= 462. Å		7.7 Å/pix.
x 60 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 170.0
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)133.938340000000011 (±23.098379999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 462.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human sperm flagellum end piece

EntireName: Human sperm flagellum end piece
Components
  • Organelle or cellular component: Human sperm flagellum end piece

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Supramolecule #1: Human sperm flagellum end piece

SupramoleculeName: Human sperm flagellum end piece / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
DetailsEjaculate applied directly to EM grid after collection.

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 1.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Number subtomograms used: 1940
ExtractionNumber tomograms: 2 / Number images used: 1940
Final angle assignmentType: NOT APPLICABLE

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