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Yorodumi- EMDB-35823: Cryo-EM structure of the 48-nm repeat doublet microtubule from mo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35823 | |||||||||
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Title | Cryo-EM structure of the 48-nm repeat doublet microtubule from mouse sperm | |||||||||
Map data | ||||||||||
Sample |
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Keywords | doublet microtubule / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information male germ-line stem cell population maintenance / axonemal microtubule doublet inner sheath / outer dense fiber / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / sperm flagellum assembly / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly ...male germ-line stem cell population maintenance / axonemal microtubule doublet inner sheath / outer dense fiber / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / sperm flagellum assembly / establishment of left/right asymmetry / 9+0 motile cilium / 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 / regulation of brood size / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath / regulation of calcineurin-NFAT signaling cascade / inner dynein arm assembly / Intraflagellar transport / axonemal A tubule inner sheath / Carboxyterminal post-translational modifications of tubulin / sperm axoneme assembly / protein polyglutamylation / positive regulation of feeding behavior / sperm principal piece / COPI-independent Golgi-to-ER retrograde traffic / cerebrospinal fluid circulation / cilium-dependent cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cilium movement involved in extracellular fluid movement / MAP kinase tyrosine/serine/threonine phosphatase activity / cilium movement involved in cell motility / regulation of cilium beat frequency involved in ciliary motility / regulation of store-operated calcium entry / COPI-mediated anterograde transport / Aggrephagy / protein localization to organelle / intraciliary transport / 9+2 motile cilium / Transferases; Transferring phosphorus-containing groups / Kinesins / acrosomal membrane / PKR-mediated signaling / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / ciliary transition zone / cilium movement / RHO GTPases activate IQGAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / calcium ion sensor activity / axoneme assembly / Recycling pathway of L1 / axonemal microtubule / sperm DNA condensation / left/right axis specification / cilium organization / COPI-dependent Golgi-to-ER retrograde traffic / flagellated sperm motility / RHO GTPases Activate Formins / gamma-tubulin ring complex / Separation of Sister Chromatids / 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 / Regulation of PLK1 Activity at G2/M Transition / manchette / positive regulation of cilium assembly / MHC class II antigen presentation / protein targeting to mitochondrion / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / protein targeting to membrane / GTP biosynthetic process / microtubule organizing center / intermediate filament / nucleoside diphosphate kinase activity / ciliary base / extrinsic component of membrane / receptor clustering / tubulin complex / intercellular bridge / myosin phosphatase activity / protein-serine/threonine phosphatase / regulation of neuron projection development / AMP binding / beta-tubulin binding / regulation of cell division / phosphatase activity / axoneme / phosphoprotein phosphatase activity / microtubule-based process / mitotic cytokinesis Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhou LN / Gui M / Wu JP | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell / Year: 2023 Title: Structures of sperm flagellar doublet microtubules expand the genetic spectrum of male infertility. Authors: Lunni Zhou / Haobin Liu / Siyu Liu / Xiaoyu Yang / Yue Dong / Yun Pan / Zhuang Xiao / Beihong Zheng / Yan Sun / Pengyu Huang / Xixi Zhang / Jin Hu / Rui Sun / Shan Feng / Yi Zhu / Mingxi Liu ...Authors: Lunni Zhou / Haobin Liu / Siyu Liu / Xiaoyu Yang / Yue Dong / Yun Pan / Zhuang Xiao / Beihong Zheng / Yan Sun / Pengyu Huang / Xixi Zhang / Jin Hu / Rui Sun / Shan Feng / Yi Zhu / Mingxi Liu / Miao Gui / Jianping Wu / Abstract: Sperm motility is crucial for successful fertilization. Highly decorated doublet microtubules (DMTs) form the sperm tail skeleton, which propels the movement of spermatozoa. Using cryo-electron ...Sperm motility is crucial for successful fertilization. Highly decorated doublet microtubules (DMTs) form the sperm tail skeleton, which propels the movement of spermatozoa. Using cryo-electron microscopy (cryo-EM) and artificial intelligence (AI)-based modeling, we determined the structures of mouse and human sperm DMTs and built an atomic model of the 48-nm repeat of the mouse sperm DMT. Our analysis revealed 47 DMT-associated proteins, including 45 microtubule inner proteins (MIPs). We identified 10 sperm-specific MIPs, including seven classes of Tektin5 in the lumen of the A tubule and FAM166 family members that bind the intra-tubulin interfaces. Interestingly, the human sperm DMT lacks some MIPs compared with the mouse sperm DMT. We also discovered variants in 10 distinct MIPs associated with a subtype of asthenozoospermia characterized by impaired sperm motility without evident morphological abnormalities. Our study highlights the conservation and tissue/species specificity of DMTs and expands the genetic spectrum of male infertility. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35823.map.gz | 325.1 MB | EMDB map data format | |
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Header (meta data) | emd-35823-v30.xml emd-35823.xml | 80.1 KB 80.1 KB | Display Display | EMDB header |
Images | emd_35823.png | 153.3 KB | ||
Filedesc metadata | emd-35823.cif.gz | 19.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35823 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35823 | HTTPS FTP |
-Related structure data
Related structure data | 8iyjMC 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_35823.map.gz / Format: CCP4 / Size: 689 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Mouse sperm DMT
+Supramolecule #1: Mouse sperm DMT
+Macromolecule #1: Cilia- and flagella-associated protein 95
+Macromolecule #2: EF-hand domain-containing family member B
+Macromolecule #3: Cilia- and flagella-associated protein 53
+Macromolecule #4: Nucleoside diphosphate kinase 7
+Macromolecule #5: Cilia- and flagella-associated protein 107
+Macromolecule #6: Cilia- and flagella-associated protein 141
+Macromolecule #7: Tektin-1
+Macromolecule #8: Tubulin alpha-3 chain
+Macromolecule #9: Tubulin beta-4B chain
+Macromolecule #10: Meiosis-specific nuclear structural protein 1
+Macromolecule #11: Tektin-2
+Macromolecule #12: Tektin-3
+Macromolecule #13: Sperm-associated antigen 8
+Macromolecule #14: Tektin-4
+Macromolecule #15: Cilia- and flagella-associated protein 161
+Macromolecule #16: Piercer of microtubule wall 2 protein
+Macromolecule #17: Protein FAM166A
+Macromolecule #18: Cilia- and flagella-associated protein 68
+Macromolecule #19: Cilia and flagella-associated protein 77
+Macromolecule #20: Family with sequence similarity 183, member B
+Macromolecule #21: Cilia- and flagella-associated protein 90
+Macromolecule #22: Protein FAM166C
+Macromolecule #23: RIB43A-like with coiled-coils protein 1
+Macromolecule #24: Dual specificity phosphatase 21
+Macromolecule #25: EF-hand domain-containing protein 1
+Macromolecule #26: Testis expressed 49
+Macromolecule #27: Testis-expressed sequence 37 protein
+Macromolecule #28: Tektin bundle-interacting protein 1
+Macromolecule #29: RIB43A-like with coiled-coils protein 2
+Macromolecule #30: Tektin-5
+Macromolecule #31: EF-hand domain-containing family member C2
+Macromolecule #32: Spermatid-specific manchette-related protein 1
+Macromolecule #33: Protein phosphatase 1 regulatory subunit 32
+Macromolecule #34: Testis-specific serine/threonine-protein kinase 6
+Macromolecule #35: Cilia- and flagella-associated protein 20
+Macromolecule #36: Outer dense fiber protein 3
+Macromolecule #37: Parkin coregulated gene protein homolog
+Macromolecule #38: Testis, prostate and placenta-expressed protein
+Macromolecule #39: Cilia- and flagella-associated protein 45
+Macromolecule #40: Uncharacterized protein C10orf82 homolog
+Macromolecule #41: Coiled-coil domain-containing protein 105
+Macromolecule #42: Cilia- and flagella-associated protein 52
+Macromolecule #43: Enkurin
+Macromolecule #44: Testis-expressed protein 43
+Macromolecule #45: Protein Flattop
+Macromolecule #46: EF-hand calcium-binding domain-containing protein 6
+Macromolecule #47: Cilia- and flagella-associated protein 210
+Macromolecule #48: Cilia- and flagella-associated protein 276
+Macromolecule #49: Piercer of microtubule wall 1 protein
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 25135 / Average exposure time: 2.56 sec. / Average electron dose: 50.0 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: 2.6 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95290 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |