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Yorodumi- PDB-8i7r: In situ structure of axonemal doublet microtubules in mouse sperm... -
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-Basic information
Entry | Database: PDB / ID: 8i7r | ||||||
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Title | In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / microtubules / axoneme / sperm / filament | ||||||
Function / homology | Function and homology information male germ-line stem cell population maintenance / protein localization to motile cilium / left/right pattern formation / 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 ...male germ-line stem cell population maintenance / protein localization to motile cilium / left/right pattern formation / 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 / regulation of calcineurin-NFAT signaling cascade / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / Intraflagellar transport / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / positive regulation of feeding behavior / regulation of cilium beat frequency involved in ciliary motility / cerebrospinal fluid circulation / sperm principal piece / COPI-independent Golgi-to-ER retrograde traffic / MAP kinase tyrosine/serine/threonine phosphatase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cilium movement involved in extracellular fluid movement / intraciliary transport / cilium movement involved in cell motility / 9+2 motile cilium / regulation of store-operated calcium entry / PKR-mediated signaling / COPI-mediated anterograde transport / Transferases; Transferring phosphorus-containing groups / cilium movement / protein localization to organelle / Aggrephagy / calcium ion sensor activity / acrosomal membrane / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / axoneme assembly / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / axonemal microtubule / cilium organization / Recycling pathway of L1 / left/right axis specification / gamma-tubulin ring complex / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic / 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 / manchette / Regulation of PLK1 Activity at G2/M Transition / 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 / protein targeting to membrane / determination of left/right symmetry / GTP biosynthetic process / intermediate filament / microtubule organizing center / nucleoside diphosphate kinase activity / tubulin complex / ciliary base / myosin phosphatase activity / extrinsic component of membrane / intercellular bridge / beta-tubulin binding / receptor clustering / protein-serine/threonine phosphatase / regulation of neuron projection development / regulation of cell division / AMP binding / single fertilization / spermatid development / axoneme / phosphatase activity / cerebral cortex cell migration / alpha-tubulin binding / mitotic cytokinesis / cilium assembly / centriolar satellite / cellular response to UV-C / sperm flagellum / cellular response to unfolded protein / cytoplasmic microtubule Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.5 Å | ||||||
Authors | Zhu, Y. / Yin, G.L. / Tai, L.H. / Sun, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2023 Title: In-cell structural insight into the stability of sperm microtubule doublet. Authors: Linhua Tai / Guoliang Yin / Xiaojun Huang / Fei Sun / Yun Zhu / Abstract: The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. ...The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i7r.cif.gz | 27.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8i7r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8i7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/8i7r ftp://data.pdbj.org/pub/pdb/validation_reports/i7/8i7r | HTTPS FTP |
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-Related structure data
Related structure data | 35230MC 8i7oC C: citing same article (ref.) M: map data used to model this data |
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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 , 24 types, 416 molecules ABA1A2A3A4ABADAFAHAJALBBBDBFBHBJBLCBCDCFCHCJCLDBDDDFDHDJDL...
-EF-hand domain-containing family member ... , 2 types, 5 molecules EFG4G5G6
#9: Protein | Mass: 95891.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8CDU5 #14: Protein | Mass: 87758.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D485 |
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-Cilia- and flagella-associated protein ... , 10 types, 27 molecules GHIJKLN1N2N3N4P1P2P3UVWXXAXBXCXDXEXFXGYZa
#12: Protein | Mass: 62036.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D439 #16: Protein | | Mass: 26633.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC3 #18: Protein | | Mass: 23062.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q4KKZ1 #20: Protein | Mass: 34433.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8Y0 #26: Protein | Mass: 18960.092 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAD0 #29: Protein | Mass: 68322.164 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5F201 #33: Protein | Mass: 65962.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9U9 #34: Protein | Mass: 22781.389 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BTU1 #36: Protein | Mass: 65266.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0JLY1 #38: Protein | | Mass: 12278.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9D9 |
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-Piercer of microtubule wall ... , 2 types, 2 molecules MN
#23: Protein | Mass: 18862.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5BN45 |
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#25: Protein | Mass: 13728.513 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: V9GXK1 |
-Non-polymers , 1 types, 279 molecules
#39: Chemical | ChemComp-GTP / |
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-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: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: mouse sperm / Type: CELL / Entity ID: #1-#38 / Source: NATURAL |
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Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 117 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.6/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17450 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 689 / Num. of volumes extracted: 17450 |