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Yorodumi- EMDB-11942: "Tubulin glycylation controls axonemal dynein activity, flagellar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11942 | |||||||||
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Title | "Tubulin glycylation controls axonemal dynein activity, flagellar beat and male fertility": Pre-pre-power stroke conformation of the mouse sperm outer dynein arms (ODAs). Both beta- and gamma-heavy chains are in pre-power stroke conformation. Cryo-ET, classification and sub-tomogram averaging. | |||||||||
Map data | Pre-pre-power stroke conformation of the mouse sperm outer dynein arms (ODAs). Both %u03B2- and %u03B3-heavy chains are in pre-power stroke conformation. Cryo-ET, classification and sub-tomogram averaging. | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 24.7 Å | |||||||||
Authors | Gadadhar S / Alvarez Viar G / Hansen JN / Gong A / Kostarev A / Ialy-Radio C / Leboucher S / Whitfield M / Ziyyat A / Toure A ...Gadadhar S / Alvarez Viar G / Hansen JN / Gong A / Kostarev A / Ialy-Radio C / Leboucher S / Whitfield M / Ziyyat A / Toure A / Alvarez L / Pigino G / Janke C | |||||||||
Funding support | 1 items
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Citation | Journal: Science / Year: 2021 Title: Tubulin glycylation controls axonemal dynein activity, flagellar beat, and male fertility. Authors: Sudarshan Gadadhar / Gonzalo Alvarez Viar / Jan Niklas Hansen / An Gong / Aleksandr Kostarev / Côme Ialy-Radio / Sophie Leboucher / Marjorie Whitfield / Ahmed Ziyyat / Aminata Touré / Luis ...Authors: Sudarshan Gadadhar / Gonzalo Alvarez Viar / Jan Niklas Hansen / An Gong / Aleksandr Kostarev / Côme Ialy-Radio / Sophie Leboucher / Marjorie Whitfield / Ahmed Ziyyat / Aminata Touré / Luis Alvarez / Gaia Pigino / Carsten Janke / Abstract: Posttranslational modifications of the microtubule cytoskeleton have emerged as key regulators of cellular functions, and their perturbations have been linked to a growing number of human pathologies. ...Posttranslational modifications of the microtubule cytoskeleton have emerged as key regulators of cellular functions, and their perturbations have been linked to a growing number of human pathologies. Tubulin glycylation modifies microtubules specifically in cilia and flagella, but its functional and mechanistic roles remain unclear. In this study, we generated a mouse model entirely lacking tubulin glycylation. Male mice were subfertile owing to aberrant beat patterns of their sperm flagella, which impeded the straight swimming of sperm cells. Using cryo-electron tomography, we showed that lack of glycylation caused abnormal conformations of the dynein arms within sperm axonemes, providing the structural basis for the observed dysfunction. Our findings reveal the importance of microtubule glycylation for controlled flagellar beating, directional sperm swimming, and male fertility. | |||||||||
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_11942.map.gz | 643.2 KB | EMDB map data format | |
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Header (meta data) | emd-11942-v30.xml emd-11942.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_11942.png | 45.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11942 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11942 | HTTPS FTP |
-Validation report
Summary document | emd_11942_validation.pdf.gz | 222.2 KB | Display | EMDB validaton report |
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Full document | emd_11942_full_validation.pdf.gz | 221.4 KB | Display | |
Data in XML | emd_11942_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11942 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11942 | 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_11942.map.gz / Format: CCP4 / Size: 695.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Pre-pre-power stroke conformation of the mouse sperm outer dynein arms (ODAs). Both %u03B2- and %u03B3-heavy chains are in pre-power stroke conformation. Cryo-ET, classification and sub-tomogram averaging. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.422 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 : axonemal outer dynein arm (ODA)
Entire | Name: axonemal outer dynein arm (ODA) |
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Components |
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-Supramolecule #1: axonemal outer dynein arm (ODA)
Supramolecule | Name: axonemal outer dynein arm (ODA) / type: complex / ID: 1 / Parent: 0 Details: Pre-pre-power stroke conformation of the mouse sperm outer dynein arms (ODAs). Both beta- and gamma- heavy chains are in pre-power stroke conformation. Reconstructed with cryo-ET, ...Details: Pre-pre-power stroke conformation of the mouse sperm outer dynein arms (ODAs). Both beta- and gamma- heavy chains are in pre-power stroke conformation. Reconstructed with cryo-ET, classification and sub-tomogram averaging. |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: Wild type / Tissue: Sperm cell / Organelle: flagellum |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Component - Name: PBS |
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Grid | Model: Quantifoil R3.5/1 / Material: GOLD / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 24.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1426 |
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Extraction | Number tomograms: 7 / Number images used: 1426 |
Final angle assignment | Type: NOT APPLICABLE |
Crystal parameters | Unit cell - A: 76 Å / Unit cell - B: 60 Å / Unit cell - C: 39 Å / Unit cell - C sampling length: 1 Å / Unit cell - γ: 90 ° / Plane group: C 1 2 |