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Yorodumi- EMDB-12067: triplet microtubule from the proximal region of the pig sperm pro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12067 | |||||||||
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Title | triplet microtubule from the proximal region of the pig sperm proximal centriole | |||||||||
Map data | subtomogram average of triplet microtubules from the proximal region of the pig sperm proximal centriole | |||||||||
Sample |
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Biological species | Sus scrofa domesticus (domestic pig) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 30.0 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_12067.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-12067-v30.xml emd-12067.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_12067.png | 109.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12067 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12067 | HTTPS FTP |
-Validation report
Summary document | emd_12067_validation.pdf.gz | 228.5 KB | Display | EMDB validaton report |
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Full document | emd_12067_full_validation.pdf.gz | 227.6 KB | Display | |
Data in XML | emd_12067_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12067 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12067 | 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_12067.map.gz / Format: CCP4 / Size: 1.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | subtomogram average of triplet microtubules from the proximal region of the pig sperm proximal centriole | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.68 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 : triplet microtubules from the proximal region of the pig sperm pr...
Entire | Name: triplet microtubules from the proximal region of the pig sperm proximal centriole |
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Components |
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-Supramolecule #1: triplet microtubules from the proximal region of the pig sperm pr...
Supramolecule | Name: triplet microtubules from the proximal region of the pig sperm proximal centriole type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Sus scrofa domesticus (domestic pig) / Tissue: sperm / Organelle: centriole / Location in cell: sperm neck |
-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 |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 200 |
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Extraction | Number tomograms: 3 / Number images used: 200 / Software - Name: PEET (ver. 1.13.0) |
CTF correction | Software - Name: PEET (ver. 1.13.0) |
Final angle assignment | Type: OTHER / Software - Name: PEET (ver. 1.13.0) |