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- EMDB-41431: 48-nm repeating structure of doublets from mouse sperm flagella -
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Open data
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Basic information
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Title | 48-nm repeating structure of doublets from mouse sperm flagella | ||||||||||||
![]() | Final map of 48 nm-repeating unit of mouse sperm doublets | ||||||||||||
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![]() | Mammalian sperm / axoneme / microtubule-based structure / microtubule inner protein / non-motor proteins / cellular motility / fertility / structural protein | ||||||||||||
Function / homology | ![]() ERKs are inactivated / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / left/right pattern formation / axonemal microtubule doublet inner sheath / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size ...ERKs are inactivated / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / left/right pattern formation / axonemal microtubule doublet inner sheath / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / 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 / protein localization to motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / Intraflagellar transport / manchette / Carboxyterminal post-translational modifications of tubulin / sperm axoneme assembly / protein polyglutamylation / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / positive regulation of feeding behavior / regulation of microtubule nucleation / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cerebrospinal fluid circulation / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / epithelial cilium movement involved in extracellular fluid movement / protein tyrosine/serine/threonine phosphatase activity / cilium movement involved in cell motility / COPI-mediated anterograde transport / Aggrephagy / regulation of store-operated calcium entry / Transferases; Transferring phosphorus-containing groups / Kinesins / 9+2 motile cilium / intraciliary transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / acrosomal membrane / microtubule sliding / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / ciliary transition zone / cilium movement / RHO GTPases activate IQGAPs / Recycling pathway of L1 / axoneme assembly / left/right axis specification / organelle transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / calcium ion sensor activity / RHO GTPases Activate Formins / axonemal microtubule / Separation of Sister Chromatids / cilium organization / Hedgehog 'off' state / 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 / forebrain morphogenesis / gamma-tubulin ring complex / glial cell differentiation / Regulation of PLK1 Activity at G2/M Transition / neuron projection arborization / cerebellar cortex morphogenesis / flagellated sperm motility / positive regulation of cilium assembly / dentate gyrus development / cell projection organization / MHC class II antigen presentation / UTP biosynthetic process / CTP biosynthetic process / centrosome cycle / determination of left/right symmetry / pyramidal neuron differentiation / intermediate filament / motor behavior / nucleoside diphosphate kinase activity / regulation of focal adhesion assembly / GTP biosynthetic process / positive regulation of cell motility / tubulin complex / response to L-glutamate / smoothened signaling pathway / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.7 Å | ||||||||||||
![]() | Chen Z / Shiozak M / Hass KM / Skinner W / Zhao S / Guo C / Polacco BJ / Yu Z / Krogan NJ / Kaake RM ...Chen Z / Shiozak M / Hass KM / Skinner W / Zhao S / Guo C / Polacco BJ / Yu Z / Krogan NJ / Kaake RM / Vale RD / Agard DA | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking. Authors: Zhen Chen / Momoko Shiozaki / Kelsey M Haas / Will M Skinner / Shumei Zhao / Caiying Guo / Benjamin J Polacco / Zhiheng Yu / Nevan J Krogan / Polina V Lishko / Robyn M Kaake / Ronald D Vale / David A Agard / ![]() Abstract: To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their ...To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their structures in vitro. Here, we combined cellular cryoelectron tomography (cryo-ET) and AlphaFold2 modeling to address these questions and understand how mammalian sperm are built in situ. Our cellular cryo-ET and subtomogram averaging provided 6.0-Å reconstructions of axonemal microtubule structures. The well-resolved tertiary structures allowed us to unbiasedly match sperm-specific densities with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105, and SPACA9 as novel microtubule-associated proteins. These proteins form an extensive interaction network crosslinking the lumen of axonemal doublet microtubules, suggesting their roles in modulating the mechanical properties of the filaments. Indeed, Tekt5 -/- sperm possess more deformed flagella with 180° bends. Together, our studies presented a cellular visual proteomics workflow and shed light on the in vivo functions of Tektin 5. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 54.2 KB 54.2 KB | Display Display | ![]() |
Images | ![]() | 136 KB | ||
Filedesc metadata | ![]() | 16.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 566.8 KB | Display | ![]() |
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Full document | ![]() | 566.4 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8to0MC 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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Annotation | Final map of 48 nm-repeating unit of mouse sperm doublets | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Mouse sperm
+Supramolecule #1: Mouse sperm
+Macromolecule #1: Cilia- and flagella-associated protein 95
+Macromolecule #2: Tektin-1
+Macromolecule #3: Detyrosinated tubulin alpha-1A chain
+Macromolecule #4: Tubulin beta-4B chain
+Macromolecule #5: Tektin-2
+Macromolecule #6: EF-hand domain-containing family member B
+Macromolecule #7: Tektin-3
+Macromolecule #8: Meiosis-specific nuclear structural protein 1
+Macromolecule #9: Tektin-4
+Macromolecule #10: Cilia- and flagella-associated protein 53
+Macromolecule #11: Tektin bundle-interacting protein 1
+Macromolecule #12: Cilia- and flagella-associated protein 141
+Macromolecule #13: Nucleoside diphosphate kinase 7
+Macromolecule #14: Protein FAM166B
+Macromolecule #15: Sperm-associated antigen 8
+Macromolecule #16: RIB43A-like with coiled-coils protein 2
+Macromolecule #17: Cilia- and flagella-associated protein 107
+Macromolecule #18: Cilia- and flagella-associated protein 161
+Macromolecule #19: EF-hand domain-containing protein 1
+Macromolecule #20: Sperm acrosome-associated protein 9
+Macromolecule #21: EF-hand domain-containing family member C2
+Macromolecule #22: Cilia- and flagella-associated protein 20
+Macromolecule #23: Parkin coregulated gene protein homolog
+Macromolecule #24: Dual specificity protein phosphatase 3
+Macromolecule #25: Piercer of microtubule wall 2 protein
+Macromolecule #26: Tektin-5
+Macromolecule #27: Cilia- and flagella-associated protein 45
+Macromolecule #28: Cilia- and flagella-associated protein 52
+Macromolecule #29: Enkurin
+Macromolecule #30: Protein Flattop
+Macromolecule #31: Cilia- and flagella- associated protein 210
+Macromolecule #32: Cilia- and flagella-associated protein 276
+Macromolecule #33: EF-hand calcium-binding domain-containing protein 6
+Macromolecule #34: Coiled-coil domain-containing protein 105
+Macromolecule #35: Piercer of microtubule wall 1 protein
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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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: 4.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0-beta2) / Number subtomograms used: 12848 |
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Extraction | Number tomograms: 76 / Number images used: 32288 Details: 32288 particles were initially picked every 24 nm along the microtubules. |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |