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Yorodumi- EMDB-35230: In situ structure of axonemal doublet microtubules in mouse sperm... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35230 | |||||||||
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Title | In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat | |||||||||
Map data | In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat | |||||||||
Sample |
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Keywords | microtubules / axoneme / sperm / filament / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information male germ-line stem cell population maintenance / protein localization to motile cilium / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly ...male germ-line stem cell population maintenance / protein localization to motile cilium / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / regulation of calcineurin-NFAT signaling cascade / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / positive regulation of feeding behavior / cerebrospinal fluid circulation / regulation of cilium beat frequency involved in ciliary motility / sperm principal piece / COPI-independent Golgi-to-ER retrograde traffic / MAP kinase tyrosine/serine/threonine phosphatase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cilium movement involved in extracellular fluid movement / intraciliary transport / cilium movement involved in cell motility / 9+2 motile cilium / regulation of store-operated calcium entry / PKR-mediated signaling / COPI-mediated anterograde transport / cilium movement / protein localization to organelle / Aggrephagy / Transferases; Transferring phosphorus-containing groups / calcium ion sensor activity / acrosomal membrane / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / axoneme assembly / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / cilium organization / Recycling pathway of L1 / axonemal microtubule / left/right axis specification / COPI-dependent Golgi-to-ER retrograde traffic / gamma-tubulin ring complex / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / manchette / positive regulation of cilium assembly / MHC class II antigen presentation / protein targeting to mitochondrion / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / protein targeting to membrane / determination of left/right symmetry / GTP biosynthetic process / intermediate filament / microtubule organizing center / nucleoside diphosphate kinase activity / tubulin complex / ciliary base / myosin phosphatase activity / extrinsic component of membrane / intercellular bridge / beta-tubulin binding / protein-serine/threonine phosphatase / receptor clustering / regulation of neuron projection development / AMP binding / regulation of cell division / single fertilization / axoneme / phosphatase activity / spermatid development / cerebral cortex cell migration / mitotic cytokinesis / alpha-tubulin binding / centriolar satellite / cilium assembly / cellular response to UV-C / sperm flagellum / cellular response to unfolded protein / cytoplasmic microtubule Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Zhu Y / Yin GL / Tai LH / Sun F | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2023 Title: In-cell structural insight into the stability of sperm microtubule doublet. Authors: Linhua Tai / Guoliang Yin / Xiaojun Huang / Fei Sun / Yun Zhu / Abstract: The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. ...The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35230.map.gz | 56.3 MB | EMDB map data format | |
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Header (meta data) | emd-35230-v30.xml emd-35230.xml | 57.4 KB 57.4 KB | Display Display | EMDB header |
Images | emd_35230.png | 165.9 KB | ||
Filedesc metadata | emd-35230.cif.gz | 16.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35230 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35230 | HTTPS FTP |
-Related structure data
Related structure data | 8i7rMC 8i7oC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35230.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.76 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : mouse sperm
+Supramolecule #1: mouse sperm
+Macromolecule #1: Meiosis-specific nuclear structural protein 1
+Macromolecule #2: Tektin-1
+Macromolecule #3: Tubulin beta-4B chain
+Macromolecule #4: Detyrosinated tubulin alpha-3 chain
+Macromolecule #5: Tektin-2
+Macromolecule #6: Nucleoside diphosphate kinase 7
+Macromolecule #7: Tektin-3
+Macromolecule #8: Tektin-4
+Macromolecule #9: EF-hand domain-containing family member B
+Macromolecule #10: Tektin bundle-interacting protein 1
+Macromolecule #11: Tektin-5
+Macromolecule #12: Cilia- and flagella-associated protein 53
+Macromolecule #13: EF-hand domain-containing protein 1
+Macromolecule #14: EF-hand domain-containing family member C2
+Macromolecule #15: Protein FAM166A
+Macromolecule #16: Cilia- and flagella-associated protein 95
+Macromolecule #17: Protein FAM166C
+Macromolecule #18: Cilia- and flagella-associated protein 107
+Macromolecule #19: Dual specificity phosphatase 21
+Macromolecule #20: Cilia- and flagella-associated protein 161
+Macromolecule #21: Coiled-coil domain-containing protein 105
+Macromolecule #22: Enkurin
+Macromolecule #23: Piercer of microtubule wall 1 protein
+Macromolecule #24: Testis-expressed protein 43
+Macromolecule #25: Piercer of microtubule wall 2 protein
+Macromolecule #26: Cilia- and flagella-associated protein 276
+Macromolecule #27: RIB43A-like with coiled-coils protein 2
+Macromolecule #28: Protein Flattop
+Macromolecule #29: Cilia- and flagella-associated protein 52
+Macromolecule #30: EF-hand calcium-binding domain-containing protein 6
+Macromolecule #31: Cilia and flagella-associated protein 77
+Macromolecule #32: Sperm-associated antigen 8
+Macromolecule #33: Cilia- and flagella-associated protein 45
+Macromolecule #34: Cilia- and flagella-associated protein 20
+Macromolecule #35: Parkin coregulated gene protein homolog
+Macromolecule #36: Cilia- and flagella-associated protein 210
+Macromolecule #37: Sperm acrosome-associated protein 9
+Macromolecule #38: Cilia- and flagella-associated protein 141
+Macromolecule #39: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 689 / Number images used: 17450 |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 17450 |