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- EMDB-12079: the 96-nm axonemal repeat from horse sperm flagella (+ODF class) -

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Basic information

Entry
Database: EMDB / ID: EMD-12079
Titlethe 96-nm axonemal repeat from horse sperm flagella (+ODF class)
Map datasubtomogram average of the 96-nm axonemal repeat from horse sperm flagella ( ODF class)
Sample
  • Cell: subtomogram average of the 96-nm axonemal repeat from horse sperm flagella (+ODF class)
Biological speciesEquus caballus (horse)
Methodsubtomogram averaging / cryo EM / Resolution: 49.0 Å
AuthorsLeung MR / Zeev-Ben-Mordehai T
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)740.018.007 Netherlands
Citation
Journal: EMBO J / Year: 2021
Title: The multi-scale architecture of mammalian sperm flagella and implications for ciliary motility.
Authors: Miguel Ricardo Leung / Marc C Roelofs / Ravi Teja Ravi / Paula Maitan / Heiko Henning / Min Zhang / Elizabeth G Bromfield / Stuart C Howes / Bart M Gadella / Hermes Bloomfield-Gadêlha / ...Authors: Miguel Ricardo Leung / Marc C Roelofs / Ravi Teja Ravi / Paula Maitan / Heiko Henning / Min Zhang / Elizabeth G Bromfield / Stuart C Howes / Bart M Gadella / Hermes Bloomfield-Gadêlha / Tzviya Zeev-Ben-Mordehai /
Abstract: Motile cilia are molecular machines used by a myriad of eukaryotic cells to swim through fluid environments. However, available molecular structures represent only a handful of cell types, limiting ...Motile cilia are molecular machines used by a myriad of eukaryotic cells to swim through fluid environments. However, available molecular structures represent only a handful of cell types, limiting our understanding of how cilia are modified to support motility in diverse media. Here, we use cryo-focused ion beam milling-enabled cryo-electron tomography to image sperm flagella from three mammalian species. We resolve in-cell structures of centrioles, axonemal doublets, central pair apparatus, and endpiece singlets, revealing novel protofilament-bridging microtubule inner proteins throughout the flagellum. We present native structures of the flagellar base, which is crucial for shaping the flagellar beat. We show that outer dense fibers are directly coupled to microtubule doublets in the principal piece but not in the midpiece. Thus, mammalian sperm flagella are ornamented across scales, from protofilament-bracing structures reinforcing microtubules at the nano-scale to accessory structures that impose micron-scale asymmetries on the entire assembly. Our structures provide vital foundations for linking molecular structure to ciliary motility and evolution.
#1: Journal: Biorxiv / Year: 2020
Title: The multi-scale architecture of mammalian sperm flagella and implications for ciliary motility
Authors: Leung MR / Roelofs MC / Ravi RT / Maitan P / Zhang M / Henning H / Bromfield EG / Howes SC / Gadella BM / Bloomfield-Gadelha H / Zeev-Ben-Mordehai T
History
DepositionDec 9, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12079.png

Downloads & links

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Map

FileDownload / File: emd_12079.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of the 96-nm axonemal repeat from horse sperm flagella ( ODF class)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.32 Å/pix.
x 100 pix.
= 1132. Å		11.32 Å/pix.
x 100 pix.
= 1132. Å		11.32 Å/pix.
x 100 pix.
= 1132. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 11.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.7589375 - 0.7198494
Average (Standard dev.)0.005724321 (±0.093029626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 1132.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z11.3211.3211.32
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z1132.0001132.0001132.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.7590.7200.006

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Supplemental data

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Sample components

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Entire : subtomogram average of the 96-nm axonemal repeat from horse sperm...

EntireName: subtomogram average of the 96-nm axonemal repeat from horse sperm flagella (+ODF class)
Components
  • Cell: subtomogram average of the 96-nm axonemal repeat from horse sperm flagella (+ODF class)

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Supramolecule #1: subtomogram average of the 96-nm axonemal repeat from horse sperm...

SupramoleculeName: subtomogram average of the 96-nm axonemal repeat from horse sperm flagella (+ODF class)
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Equus caballus (horse) / Tissue: sperm

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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 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.67 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 49.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.13.0) / Number subtomograms used: 466
ExtractionNumber tomograms: 16 / Number images used: 634 / Software - Name: PEET (ver. 1.13.0)
CTF correctionSoftware - Name: PEET (ver. 1.13.0)
Final 3D classificationNumber classes: 2 / Software - Name: PEET (ver. 1.13.0)
Details: Classification was focused on the connection between the outer dense fibers (ODF) and the microtubule doublet.
Final angle assignmentType: OTHER

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