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Yorodumi- EMDB-41431: 48-nm repeating structure of doublets from mouse sperm flagella -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41431 | ||||||||||||
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Title | 48-nm repeating structure of doublets from mouse sperm flagella | ||||||||||||
Map data | Final map of 48 nm-repeating unit of mouse sperm doublets | ||||||||||||
Sample |
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Keywords | Mammalian sperm / axoneme / microtubule-based structure / microtubule inner protein / non-motor proteins / cellular motility / fertility / structural protein | ||||||||||||
Function / homology | Function and homology information ERKs are inactivated / 9+0 motile cilium / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly ...ERKs are inactivated / 9+0 motile cilium / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / left/right pattern formation / axonemal B tubule inner sheath / axonemal A tubule inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / regulation of calcineurin-NFAT signaling cascade / MAP kinase phosphatase activity / inner dynein arm assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / positive regulation of feeding behavior / cerebrospinal fluid circulation / sperm axoneme assembly / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / sperm principal piece / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / regulation of store-operated calcium entry / epithelial cilium movement involved in extracellular fluid movement / 9+2 motile cilium / intraciliary transport / PKR-mediated signaling / negative regulation of chemotaxis / COPI-mediated anterograde transport / calcium ion sensor activity / Aggrephagy / Transferases; Transferring phosphorus-containing groups / acrosomal membrane / Kinesins / ciliary transition zone / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium movement / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / Recycling pathway of L1 / axoneme assembly / axonemal microtubule / negative regulation of T cell activation / left/right axis specification / cilium organization / COPI-dependent Golgi-to-ER retrograde traffic / gamma-tubulin ring complex / flagellated sperm motility / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / organelle transport along microtubule / glial cell differentiation / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / protein tyrosine/serine/threonine phosphatase activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / forebrain morphogenesis / neuron projection arborization / Regulation of PLK1 Activity at G2/M Transition / positive regulation of focal adhesion disassembly / manchette / cerebellar cortex morphogenesis / positive regulation of cilium assembly / dentate gyrus development / MHC class II antigen presentation / pyramidal neuron differentiation / negative regulation of JNK cascade / CTP biosynthetic process / UTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / centrosome cycle / motor behavior / GTP biosynthetic process / microtubule organizing center / response to L-glutamate / intermediate filament / regulation of neuron projection development / ciliary base / nucleoside diphosphate kinase activity / regulation of focal adhesion assembly / tubulin complex / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade / smoothened signaling pathway Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.7 Å | ||||||||||||
Authors | 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 | United States, 3 items
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Citation | Journal: Cell / Year: 2023 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 | emd_41431.map.gz | 20.4 MB | EMDB map data format | |
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Header (meta data) | emd-41431-v30.xml emd-41431.xml | 54.2 KB 54.2 KB | Display Display | EMDB header |
Images | emd_41431.png | 136 KB | ||
Filedesc metadata | emd-41431.cif.gz | 16.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41431 | HTTPS FTP |
-Validation report
Summary document | emd_41431_validation.pdf.gz | 566.8 KB | Display | EMDB validaton report |
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Full document | emd_41431_full_validation.pdf.gz | 566.4 KB | Display | |
Data in XML | emd_41431_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_41431_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41431 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41431 | HTTPS FTP |
-Related structure data
Related structure data | 8to0MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41431.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Final map of 48 nm-repeating unit of mouse sperm doublets | ||||||||||||||||||||
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
-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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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-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 |