[English] 日本語
Yorodumi- EMDB-35823: Cryo-EM structure of the 48-nm repeat doublet microtubule from mo... -
+
Open data
-
Basic information
| Entry | ![]() | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Cryo-EM structure of the 48-nm repeat doublet microtubule from mouse sperm | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | doublet microtubule / STRUCTURAL PROTEIN | |||||||||
| Function / homology | Function and homology informationmale germ-line stem cell population maintenance / protein localization to motile cilium / left/right pattern formation / axonemal microtubule doublet inner sheath / 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 / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane ...male germ-line stem cell population maintenance / protein localization to motile cilium / left/right pattern formation / axonemal microtubule doublet inner sheath / 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 / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / outer dense fiber / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / protein polyglutamylation / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / sperm axoneme assembly / regulation of microtubule nucleation / positive regulation of feeding behavior / COPI-independent Golgi-to-ER retrograde traffic / Transferases; Transferring phosphorus-containing groups / 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 / MAP kinase tyrosine/serine/threonine phosphatase activity / cerebrospinal fluid circulation / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / COPI-mediated anterograde transport / Aggrephagy / 9+2 motile cilium / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein localization to organelle / regulation of store-operated calcium entry / intraciliary transport / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / acrosomal membrane / The role of GTSE1 in G2/M progression after G2 checkpoint / axoneme assembly / RHO GTPases activate IQGAPs / microtubule sliding / Recycling pathway of L1 / cilium movement / ciliary transition zone / left/right axis specification / calcium ion sensor activity / axonemal microtubule / COPI-dependent Golgi-to-ER retrograde traffic / sperm DNA condensation / RHO GTPases Activate Formins / 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 / gamma-tubulin ring complex / Regulation of PLK1 Activity at G2/M Transition / manchette / positive regulation of cilium assembly / flagellated sperm motility / MHC class II antigen presentation / cell projection organization / UTP biosynthetic process / CTP biosynthetic process / determination of left/right symmetry / intermediate filament / protein targeting to membrane / extrinsic component of membrane / positive regulation of cell motility / nucleoside diphosphate kinase activity / protein targeting to mitochondrion / GTP biosynthetic process / tubulin complex / AMP binding / protein-serine/threonine phosphatase / ciliary base / receptor clustering / protein serine/threonine phosphatase activity / phosphatase activity / regulation of cell division / microtubule organizing center / phosphoprotein phosphatase activity / mitotic cytokinesis / cellular response to UV-C / axoneme / cilium assembly / glial cell projection Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhou LN / Gui M / Wu JP | |||||||||
| Funding support | China, 1 items
| |||||||||
Citation | Journal: Cell / Year: 2023Title: 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 |
|
-
Structure visualization
| Supplemental images |
|---|
-
Downloads & links
-EMDB archive
| Map data | emd_35823.map.gz | 325.1 MB | EMDB map data format | |
|---|---|---|---|---|
| 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 ( M: atomic model generated by this map |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| 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) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
|
-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 |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | filament |
-
Sample preparation
| Buffer | pH: 7.5 |
|---|---|
| Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
| Microscope | FEI TITAN KRIOS |
|---|---|
| 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: |
|---|---|
| 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 |
Movie
Controller
About Yorodumi



Keywords
Authors
China, 1 items
Citation



























































































Z (Sec.)
Y (Row.)
X (Col.)






















FIELD EMISSION GUN

