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Yorodumi- EMDB-12135: the 96-nm axonemal repeat from mouse sperm flagella (-ODF class) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12135 | |||||||||
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Title | the 96-nm axonemal repeat from mouse sperm flagella (-ODF class) | |||||||||
Map data | subtomogram average of the 96-nm axonemal repeat from mouse sperm flagella (-ODF class) | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 50.0 Å | |||||||||
Authors | Leung MR / Zeev-Ben-Mordehai T | |||||||||
Funding support | Netherlands, 1 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12135.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-12135-v30.xml emd-12135.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_12135.png | 25.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12135 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12135.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | subtomogram average of the 96-nm axonemal repeat from mouse sperm flagella (-ODF class) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 14.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : the 96-nm axonemal repeat from mouse sperm flagella (-ODF class)
Entire | Name: the 96-nm axonemal repeat from mouse sperm flagella (-ODF class) |
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Components |
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-Supramolecule #1: the 96-nm axonemal repeat from mouse sperm flagella (-ODF class)
Supramolecule | Name: the 96-nm axonemal repeat from mouse sperm flagella (-ODF class) type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) / Tissue: sperm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 14 / Number images used: 1112 / Software - Name: PEET (ver. 1.13.0) |
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CTF correction | Software - Name: PEET (ver. 1.13.0) |
Final 3D classification | Number classes: 2 / Software - Name: PEET (ver. 1.13.0) Details: Classification was focused on the attachment point between the outer dense fibers and the microtubule doublets. |
Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.13.0) / Number subtomograms used: 250 |