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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 / regulation of calcineurin-NFAT signaling cascade / sperm axoneme assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / : / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / positive regulation of feeding behavior / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Transferases; Transferring phosphorus-containing groups / cilium-dependent cell motility / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / MAP kinase tyrosine/serine/threonine phosphatase activity / inner dynein arm assembly / cerebrospinal fluid circulation / regulation of cilium beat frequency involved in ciliary motility / RHO GTPases Activate Formins / cilium movement involved in cell motility / MHC class II antigen presentation / regulation of store-operated calcium entry / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal membrane / axoneme assembly / cilium movement / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / axonemal microtubule / calcium ion sensor activity / Separation of Sister Chromatids / sperm DNA condensation / 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 / cilium organization / 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 / ciliary transition zone / Neutrophil degranulation / nucleoside diphosphate kinase activity / positive regulation of cell motility / GTP biosynthetic process / motile cilium / AMP binding / ciliary base / regulation of neuron projection development / protein serine/threonine phosphatase activity / cerebral cortex cell migration / microtubule organizing center / mitotic cytokinesis / cellular response to UV-C / regulation of cell division / cilium assembly / spermatid development / axoneme / glial cell projection / single fertilization / sperm flagellum / phosphatase binding / alpha-tubulin binding / beta-tubulin binding / intercellular bridge / cytoplasmic microtubule / 3'-5' exonuclease activity / Hsp70 protein binding / protein tyrosine phosphatase activity / acrosomal vesicle / mitotic spindle organization / centriole / meiotic cell cycle / Hsp90 protein binding / G protein-coupled receptor binding / structural constituent of cytoskeleton / SH3 domain binding / microtubule cytoskeleton organization 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 |
-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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Netherlands, 1 items
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Processing
FIELD EMISSION GUN

