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- EMDB-40619: cryo-EM structure of sea urchin sperm doublet microtubule (48-nm ... -
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Open data
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Basic information
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Title | cryo-EM structure of sea urchin sperm doublet microtubule (48-nm periodicity) | |||||||||
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![]() | sperm / doublet microtubule / DMT / microtubule inner protein / cilia / flagella / FAP / CFAP / MIP / MAP / cytoskeleton / tublin / sea urchin / TEX / Tektin / SAXO / ODF / SPATA / RIB / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() : / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / axoneme assembly / axonemal microtubule / cilium organization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process ...: / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / axoneme assembly / axonemal microtubule / cilium organization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary base / regulation of neuron projection development / axoneme / microtubule-based process / mitotic cytokinesis / cilium assembly / alpha-tubulin binding / sperm flagellum / phosphatase binding / Hsp70 protein binding / phosphorylation / mitotic spindle organization / acrosomal vesicle / ciliary basal body / Hsp90 protein binding / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / protein-folding chaperone binding / spermatogenesis / microtubule binding / vesicle / microtubule / calmodulin binding / cytoskeleton / hydrolase activity / neuron projection / GTPase activity / centrosome / calcium ion binding / GTP binding / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Zeng J / Zhang R | |||||||||
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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 151.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 73.9 KB 73.9 KB | Display Display | ![]() |
Images | ![]() | 121.1 KB | ||
Others | ![]() ![]() ![]() | 482.5 MB 466.3 MB 466.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8snbMC ![]() 8otzC ![]() 8ou0C M: atomic model generated by this map C: citing same article ( |
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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: 1.34 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_40619_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40619_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40619_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : sea urchin sperm doublet microtubule
+Supramolecule #1: sea urchin sperm doublet microtubule
+Macromolecule #1: CFAP96(C4orf47)
+Macromolecule #2: Coiled-coil domain-containing protein 105
+Macromolecule #3: Coiled-coil domain-containing protein 81
+Macromolecule #4: FAM166C
+Macromolecule #5: Protein FAM166B
+Macromolecule #6: CFAP144(FAM183A)
+Macromolecule #7: Outer dense fiber protein 3
+Macromolecule #8: Tex33
+Macromolecule #9: C20Orf85
+Macromolecule #10: ATP6V1FNB
+Macromolecule #11: Tex26(LOC100888047)
+Macromolecule #12: Meiosis-specific nuclear structural protein 1
+Macromolecule #13: Enkurin domain-containing protein
+Macromolecule #14: CFAP107
+Macromolecule #15: Cilia- and flagella-associated protein 126
+Macromolecule #16: Flagellar FliJ protein
+Macromolecule #17: Meiosis-specific nuclear structural protein 1
+Macromolecule #18: Cilia- and flagella-associated protein 161
+Macromolecule #19: CFA20 domain-containing protein
+Macromolecule #20: CFAP21
+Macromolecule #21: Trichohyalin-plectin-homology domain-containing protein
+Macromolecule #22: CFAP276
+Macromolecule #23: Cilia- and flagella-associated protein 45
+Macromolecule #24: Cilia- and flagella-associated protein 52
+Macromolecule #25: Trichohyalin-plectin-homology domain-containing protein
+Macromolecule #26: Nucleoside diphosphate kinase
+Macromolecule #27: Cilia- and flagella-associated protein 77
+Macromolecule #28: Cilia- and flagella-associated protein 97
+Macromolecule #29: HeLo_like_N(LOC577943)
+Macromolecule #30: Outer dense fiber protein 3
+Macromolecule #31: PACRG
+Macromolecule #32: Pierce1
+Macromolecule #33: Protein phosphatase 1 regulatory subunit 32
+Macromolecule #34: RIB35
+Macromolecule #35: RIB43A-like with coiled-coils protein 2
+Macromolecule #36: EF-hand domain-containing family member C2
+Macromolecule #37: Flagellar protofilament ribbon protein rib74
+Macromolecule #38: SAXO3(LOC115918676)
+Macromolecule #39: TEPP protein
+Macromolecule #40: SPATA48
+Macromolecule #41: Sperm-associated antigen 8
+Macromolecule #42: Testicular haploid expressed gene protein-like
+Macromolecule #43: Tektin A1
+Macromolecule #44: Tektin B1
+Macromolecule #45: Tektin C1
+Macromolecule #46: Tex43
+Macromolecule #47: Tex36(CFAP95, C9orf135)
+Macromolecule #48: CFAP90(C5orf49)
+Macromolecule #49: Tex49
+Macromolecule #50: Tex49_homologue(LOC580808)
+Macromolecule #51: CFAP68(UPF0686, C11orf1)
+Macromolecule #52: SPATA45
+Macromolecule #53: C4orf45
+Macromolecule #54: Tubulin alpha chain
+Macromolecule #55: Tubulin beta chain
+Macromolecule #56: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: 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: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127673 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |