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Yorodumi- EMDB-17187: 48-nm repeat of the native axonemal doublet microtubule from bovi... -
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Basic information
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| Title | 48-nm repeat of the native axonemal doublet microtubule from bovine sperm | |||||||||
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Keywords | microtubule / cilia / sperm / axoneme / STRUCTURAL PROTEIN | |||||||||
| Function / homology | Function and homology informationaxonemal microtubule doublet inner sheath / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath ...axonemal microtubule doublet inner sheath / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / protein polyglutamylation / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / sperm axoneme assembly / positive regulation of feeding behavior / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium-dependent cell motility / COPI-dependent Golgi-to-ER retrograde traffic / Transferases; Transferring phosphorus-containing groups / sperm principal piece / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / regulation of cilium beat frequency involved in ciliary motility / MAP kinase tyrosine/serine/threonine phosphatase activity / cerebrospinal fluid circulation / RHO GTPases Activate Formins / cilium movement involved in cell motility / regulation of store-operated calcium entry / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal membrane / axoneme assembly / cilium movement / ciliary transition zone / Aggrephagy / calcium ion sensor activity / axonemal microtubule / sperm DNA condensation / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / cilium organization / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / gamma-tubulin ring complex / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / flagellated sperm motility / UTP biosynthetic process / CTP biosynthetic process / determination of left/right symmetry / Neutrophil degranulation / positive regulation of cell motility / nucleoside diphosphate kinase activity / motile cilium / GTP biosynthetic process / AMP binding / ciliary base / regulation of neuron projection development / protein serine/threonine phosphatase activity / cerebral cortex cell migration / regulation of cell division / microtubule organizing center / mitotic cytokinesis / cellular response to UV-C / axoneme / cilium assembly / glial cell projection / spermatid development / single fertilization / sperm flagellum / phosphatase binding / alpha-tubulin binding / beta-tubulin binding / intercellular bridge / cytoplasmic microtubule / sperm midpiece / 3'-5' exonuclease activity / Hsp70 protein binding / centriole / acrosomal vesicle / protein tyrosine phosphatase activity / mitotic spindle organization / meiotic cell cycle / Hsp90 protein binding / G protein-coupled receptor binding / structural constituent of cytoskeleton Similarity search - Function | |||||||||
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| Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Leung MR / Zeng J / Zhang R / Zeev-Ben-Mordehai T | |||||||||
| Funding support | Netherlands, 1 items
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Citation | Journal: Cell / Year: 2023Title: Structural specializations of the sperm tail. Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai / ![]() Abstract: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_17187.map.gz | 277.9 MB | EMDB map data format | |
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| Header (meta data) | emd-17187-v30.xml emd-17187.xml | 114.8 KB 114.8 KB | Display Display | EMDB header |
| Images | emd_17187.png | 94 KB | ||
| Filedesc metadata | emd-17187.cif.gz | 23.2 KB | ||
| Others | emd_17187_additional_1.map.gz emd_17187_half_map_1.map.gz emd_17187_half_map_2.map.gz | 179 MB 1010.4 MB 1009.6 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17187 | HTTPS FTP |
-Validation report
| Summary document | emd_17187_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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| Full document | emd_17187_full_validation.pdf.gz | 1 MB | Display | |
| Data in XML | emd_17187_validation.xml.gz | 22.4 KB | Display | |
| Data in CIF | emd_17187_validation.cif.gz | 26.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17187 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17187 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8otzMC ![]() 8ou0C ![]() 8snbC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_17187.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: #1
| File | emd_17187_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_17187_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_17187_half_map_2.map | ||||||||||||
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Sample components
+Entire : 48-nm repeat of the native axonemal doublet microtubule from bovi...
+Supramolecule #1: 48-nm repeat of the native axonemal doublet microtubule from bovi...
+Macromolecule #1: Cilia- and flagella-associated protein 95
+Macromolecule #2: Sperm acrosome associated 9
+Macromolecule #3: Testis specific serine kinase 6
+Macromolecule #4: EF-hand domain-containing protein
+Macromolecule #5: ATP6V1F neighbor
+Macromolecule #6: Outer dense fiber of sperm tails 3 like 1
+Macromolecule #7: Outer dense fiber of sperm tails 3
+Macromolecule #8: Tubulin alpha-3 chain
+Macromolecule #9: Tubulin beta-4B chain
+Macromolecule #10: Protein Flattop
+Macromolecule #11: Cilia- and flagella-associated protein 53
+Macromolecule #12: Nucleoside diphosphate kinase 7
+Macromolecule #13: EF-hand domain-containing family member C2
+Macromolecule #14: Family with sequence similarity 166 member A
+Macromolecule #15: Protein FAM166C
+Macromolecule #16: Outer dense fiber of sperm tails 3B
+Macromolecule #17: Spermatid-specific manchette-related protein 1
+Macromolecule #18: Enkurin
+Macromolecule #19: Coiled-coil domain-containing protein 105
+Macromolecule #20: Protein phosphatase 1 regulatory subunit 32
+Macromolecule #21: RIB43A-like with coiled-coils protein 2
+Macromolecule #22: Cilia- and flagella-associated protein 107
+Macromolecule #23: Piercer of microtubule wall 1 protein
+Macromolecule #24: Piercer of microtubule wall 2 protein
+Macromolecule #25: Stabilizer of axonemal microtubules 1
+Macromolecule #26: Stabilizer of axonemal microtubules 3
+Macromolecule #27: Meiosis-specific nuclear structural protein 1
+Macromolecule #28: Tektin-3
+Macromolecule #29: Tektin-5
+Macromolecule #30: Sperm-associated antigen 8
+Macromolecule #31: Spermatogenesis-associated protein 48
+Macromolecule #32: Tektin-1
+Macromolecule #33: Tektin-2
+Macromolecule #34: Uncharacterized protein C1orf100 homolog
+Macromolecule #35: TEPP protein
+Macromolecule #36: Uncharacterized protein MGC137036
+Macromolecule #37: Testis expressed 33
+Macromolecule #38: Testis-expressed sequence 37 protein
+Macromolecule #39: Testis-expressed protein 43
+Macromolecule #40: Testis expressed 49
+Macromolecule #41: Theg spermatid protein like
+Macromolecule #42: EF-hand domain-containing family member B
+Macromolecule #43: Tektin bundle interacting protein 1
+Macromolecule #44: Tektin-4
+Macromolecule #45: Chromosome 7 open reading frame 31
+Macromolecule #46: Cilia- and flagella- associated protein 210
+Macromolecule #47: EF-hand domain-containing protein 1
+Macromolecule #48: Uncharacterized protein C10orf82 homolog
+Macromolecule #49: Cilia- and flagella-associated protein 144
+Macromolecule #50: Chromosome 20 C5orf49 homolog
+Macromolecule #51: Chromosome 19 C17orf98 homolog
+Macromolecule #52: Chromosome 13 C20orf85 homolog
+Macromolecule #53: Cilia- and flagella-associated protein 68
+Macromolecule #54: Cilia and flagella associated protein 77
+Macromolecule #55: UPF0602 protein C4orf47 homolog
+Macromolecule #56: Cilia- and flagella-associated protein 20
+Macromolecule #57: Parkin coregulated gene protein
+Macromolecule #58: CFAP97 domain containing 1
+Macromolecule #59: Cilia- and flagella-associated protein 45
+Macromolecule #60: Cilia- and flagella-associated protein 52
+Macromolecule #61: Cilia- and flagella-associated protein 141
+Macromolecule #62: Cilia- and flagella-associated protein 161
+Macromolecule #63: Dual specificity phosphatase 21
+Macromolecule #64: Uncharacterized protein C4orf45 homolog
+Macromolecule #65: Cilia- and flagella-associated protein 276
+Macromolecule #66: EF-hand calcium-binding domain-containing protein 3
+Macromolecule #67: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #68: MAGNESIUM ION
+Macromolecule #69: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | filament |
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Sample preparation
| Buffer | pH: 7.9 |
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| Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
| Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
| Microscope | FEI TALOS ARCTICA |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
| Sample stage | Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Keywords
Authors
Netherlands, 1 items
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Processing
FIELD EMISSION GUN

