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Yorodumi- PDB-8i7o: In situ structure of axonemal doublet microtubules in mouse sperm... -
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-Basic information
Entry | Database: PDB / ID: 8i7o | ||||||
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Title | In situ structure of axonemal doublet microtubules in mouse sperm with 16-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 / outer acrosomal membrane / 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 / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin ...male germ-line stem cell population maintenance / outer acrosomal membrane / 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 / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / inner dynein arm assembly / cilium-dependent cell motility / positive regulation of feeding behavior / regulation of cilium beat frequency involved in ciliary motility / 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 / cilium movement involved in cell motility / 9+2 motile cilium / PKR-mediated signaling / COPI-mediated anterograde transport / protein localization to organelle / Aggrephagy / 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 / cilium organization / Recycling pathway of L1 / axonemal microtubule / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / 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 / MHC class II antigen presentation / protein targeting to mitochondrion / motile cilium / positive regulation of cell motility / protein targeting to membrane / microtubule organizing center / tubulin complex / ciliary base / myosin phosphatase activity / extrinsic component of membrane / intercellular bridge / beta-tubulin binding / protein-serine/threonine phosphatase / regulation of neuron projection development / regulation of cell division / axoneme / phosphatase activity / spermatid development / cerebral cortex cell migration / mitotic cytokinesis / alpha-tubulin binding / cilium assembly / sperm flagellum / cellular response to unfolded protein / cytoplasmic microtubule / microtubule-based process / dephosphorylation / sperm midpiece / Hsp70 protein binding / heat shock protein binding / centriole / Neutrophil degranulation / cellular response to leukemia inhibitory factor / mitotic spindle organization / protein-tyrosine-phosphatase / acrosomal vesicle / ciliary basal body / protein tyrosine phosphatase activity / cell projection / G protein-coupled receptor binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / mitochondrial intermembrane space / protein localization / cilium / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / intracellular calcium ion homeostasis / SH3 domain binding / spindle pole Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.5 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 | 8i7o.cif.gz | 11.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8i7o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8i7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/8i7o ftp://data.pdbj.org/pub/pdb/validation_reports/i7/8i7o | HTTPS FTP |
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-Related structure data
Related structure data | 35229MC 8i7rC 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 , 19 types, 179 molecules A2A3AEAGAIBEBGBICGCIDEDGEEEGFEFGGEGGGIHEHGHIIEIGIIJEJGKEKGKI...
#1: Protein | Mass: 48713.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAJ2 #2: Protein | Mass: 48689.090 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05214 #3: Protein | Mass: 47897.918 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372 #4: Protein | Mass: 50385.066 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q922G7 #5: Protein | Mass: 56754.777 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6X6Z7 #6: Protein | Mass: 52121.449 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q149S1 #7: Protein | Mass: 23987.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A6H6Q4 #8: Protein | Mass: 62817.535 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G5E8A8 #11: Protein | Mass: 36659.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4K5 #12: Protein | Mass: 23097.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAS2 #13: Protein | Mass: 21527.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q9D9D8, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase #14: Protein | Mass: 57406.484 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4K7 #15: Protein | Mass: 29587.521 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6SP97 #16: Protein | Mass: 16305.608 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9I1 #18: Protein | Mass: 20575.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8X9 #20: Protein | Mass: 176028.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P1E8 #21: Protein | | Mass: 32786.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A087WRI3 #23: Protein | Mass: 27763.268 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAK2 #24: Protein | Mass: 19512.373 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TPM5 |
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-EF-hand domain-containing ... , 2 types, 3 molecules G1G2G5
#9: Protein | Mass: 75235.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9T8 #10: Protein | | Mass: 87758.023 Da / Num. of mol.: 1 / 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 ... , 3 types, 7 molecules N2N3P1P2XCXDXE
#17: Protein | Mass: 18960.092 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAD0 #19: Protein | Mass: 68322.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5F201 #22: Protein | Mass: 22781.389 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BTU1 |
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-Non-polymers , 1 types, 123 molecules
#25: 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-#24 / 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37018 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 689 / Num. of volumes extracted: 37018 |