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- EMDB-17187: 48-nm repeat of the native axonemal doublet microtubule from bovi... -
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Open data
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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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![]() | microtubule / cilia / sperm / axoneme / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / protein polyglutamylation / sperm axoneme assembly / positive regulation of feeding behavior ...sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / protein polyglutamylation / 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 / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / MAP kinase tyrosine/serine/threonine phosphatase activity / RHO GTPases Activate Formins / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / Transferases; Transferring phosphorus-containing groups / acrosomal membrane / MHC class II antigen presentation / ciliary transition zone / cilium movement / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / Aggrephagy / sperm DNA condensation / axonemal microtubule / cilium organization / gamma-tubulin ring complex / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / Separation of Sister Chromatids / 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 / manchette / nucleotide-activated protein kinase complex / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / UTP biosynthetic process / CTP biosynthetic process / motile cilium / negative regulation of TOR signaling / positive regulation of cell motility / determination of left/right symmetry / microtubule organizing center / Neutrophil degranulation / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary base / myosin phosphatase activity / dephosphorylation / regulation of neuron projection development / beta-tubulin binding / axoneme / mitotic cytokinesis / centriolar satellite / spermatid development / cilium assembly / alpha-tubulin binding / cellular response to UV-C / sperm flagellum / single fertilization / phosphatase binding / meiotic cell cycle / cellular response to glucose starvation / sperm midpiece / Hsp70 protein binding / 3'-5' exonuclease activity / centriole / mitotic spindle organization / acrosomal vesicle / ciliary basal body / protein tyrosine phosphatase activity / cell projection / G protein-coupled receptor binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cilium / structural constituent of cytoskeleton / mitotic spindle / spindle pole / microtubule cytoskeleton organization / SH3 domain binding / spindle / calcium-dependent protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Leung MR / Zeng J / Zhang R / Zeev-Ben-Mordehai T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 277.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 103.5 KB 103.5 KB | Display Display | ![]() |
Images | ![]() | 94 KB | ||
Filedesc metadata | ![]() | 22.7 KB | ||
Others | ![]() ![]() ![]() | 179 MB 1010.4 MB 1009.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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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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![]() | 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: ![]() |
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 |