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- EMDB-12132: singlet microtubules from the mouse sperm endpiece -

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Basic information

Entry
Database: EMDB / ID: EMD-12132
Titlesinglet microtubules from the mouse sperm endpiece
Map data
Samplesinglet microtubules from the mouse sperm endpiece
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 30 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
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 17, 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: 5.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12132.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.08 Å/pix.
x 50 pix.
= 354. Å
7.08 Å/pix.
x 50 pix.
= 354. Å
7.08 Å/pix.
x 50 pix.
= 354. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.08 Å
Density
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-18.999376 - 23.069262
Average (Standard dev.)-1.090779 (±7.204253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions505050
Spacing505050
CellA=B=C: 354.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.087.087.08
M x/y/z505050
origin x/y/z0.0000.0000.000
length x/y/z354.000354.000354.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS505050
D min/max/mean-18.99923.069-1.091

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Supplemental data

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Sample components

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Entire singlet microtubules from the mouse sperm endpiece

EntireName: singlet microtubules from the mouse sperm endpiece / Number of components: 1

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Component #1: cellular-component, singlet microtubules from the mouse sperm endpiece

Cellular-componentName: singlet microtubules from the mouse sperm endpiece / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (natural)Organ or tissue: sperm

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 1581
3D reconstructionSoftware: PEET / Resolution: 30 Å / Resolution method: FSC 0.5 CUT-OFF

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