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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 informationouter acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / axonemal microtubule doublet inner sheath / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / sperm axoneme assembly ...outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / axonemal microtubule doublet inner sheath / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / sperm axoneme assembly / protein polyglutamylation / positive regulation of feeding behavior / cerebral cortex cell migration / regulation of calcineurin-NFAT signaling cascade / Intraflagellar transport / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / MAP kinase tyrosine/serine/threonine phosphatase activity / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / regulation of store-operated calcium entry / MHC class II antigen presentation / cilium movement involved in cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal membrane / axoneme assembly / Aggrephagy / cilium movement / sperm DNA condensation / Separation of Sister Chromatids / calcium ion sensor activity / 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 / cilium organization / axonemal microtubule / Regulation of PLK1 Activity at G2/M Transition / gamma-tubulin ring complex / manchette / positive regulation of cell motility / ciliary transition zone / determination of left/right symmetry / sperm head-tail coupling apparatus / 3'-5'-DNA exonuclease activity / UTP biosynthetic process / CTP biosynthetic process / motile cilium / DNA catabolic process / Neutrophil degranulation / nucleoside diphosphate kinase activity / single fertilization / sperm principal piece / GTP biosynthetic process / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / spermatid development / AMP binding / centriolar satellite / regulation of dendrite morphogenesis / ciliary base / flagellated sperm motility / sperm end piece / protein serine/threonine phosphatase activity / microtubule organizing center / mitotic cytokinesis / regulation of cell division / axoneme / phosphatase binding / alpha-tubulin binding / sperm flagellum / cilium assembly / beta-tubulin binding / cytoplasmic microtubule / centriole / protein tyrosine phosphatase activity / acrosomal vesicle / sperm midpiece / Hsp70 protein binding / mitotic spindle organization / Hsp90 protein binding / meiotic cell cycle / SH3 domain binding / microtubule cytoskeleton organization / mitotic spindle / G protein-coupled receptor binding / spindle / structural constituent of cytoskeleton / calcium ion transport / spindle pole / microtubule cytoskeleton / cilium / mitotic cell cycle / double-stranded RNA binding / actin binding / ciliary basal body / cell body Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| 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 |
-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 | ||||||||||||||||||||||||||||||||||||
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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
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Netherlands, 1 items
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Processing
FIELD EMISSION GUN

