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Yorodumi- PDB-8ou0: bovine sperm endpiece singlet microtubules (one tubulin dimer and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ou0 | ||||||
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Title | bovine sperm endpiece singlet microtubules (one tubulin dimer and associated microtubule inner proteins) | ||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / microtubule / microtubule inner protein / sperm / cilia | ||||||
Function / homology | Function and homology information Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / cold acclimation / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / axonemal microtubule / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cilium assembly / Hedgehog 'off' state / Neutrophil degranulation / cellular response to cold / ciliary base / intercellular bridge / sperm flagellum / centriole / acrosomal vesicle / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / calcium-dependent protein binding / double-stranded RNA binding / mitotic cell cycle / microtubule binding / microtubule / protein stabilization / cytoskeleton / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Leung, M.R. / Zeev-Ben-Mordehai, T. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Cell / Year: 2023 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ou0.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ou0.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ou0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/8ou0 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/8ou0 | HTTPS FTP |
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-Related structure data
Related structure data | 17188MC 8otzC 8snbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 4 molecules BDCA
#1: Protein | Mass: 49877.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHM5 |
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#2: Protein | Mass: 54672.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3S5ZPV0 |
#3: Protein | Mass: 25174.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3Q1MYU9 |
#4: Protein | Mass: 49978.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: Q32KN8, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
-Non-polymers , 3 types, 3 molecules
#5: Chemical | ChemComp-GDP / |
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#6: Chemical | ChemComp-GTP / |
#7: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: tubulin heterodimer with associated microtubule inner proteins SPACA9 and SAXO1 Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 7.3 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240292 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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