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- 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 | ||||||
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![]() | STRUCTURAL PROTEIN / microtubules / axoneme / sperm / filament | ||||||
Function / homology | ![]() male germ-line stem cell population maintenance / 9+0 motile cilium / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / axonemal B tubule inner sheath / axonemal A tubule inner sheath ...male germ-line stem cell population maintenance / 9+0 motile cilium / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / axonemal B tubule inner sheath / axonemal A tubule inner sheath / inner dynein arm assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / positive regulation of feeding behavior / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / sperm principal piece / MAP kinase tyrosine/serine/threonine phosphatase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of cilium beat frequency involved in ciliary motility / 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 / The role of GTSE1 in G2/M progression after G2 checkpoint / Recycling pathway of L1 / axoneme assembly / axonemal microtubule / cilium organization / COPI-dependent Golgi-to-ER retrograde traffic / flagellated sperm motility / 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 / regulation of neuron projection development / ciliary base / tubulin complex / myosin phosphatase activity / intercellular bridge / extrinsic component of membrane / protein-serine/threonine phosphatase / beta-tubulin binding / regulation of cell division / axoneme / phosphatase activity / cytoplasmic microtubule / microtubule-based process / mitotic cytokinesis / spermatid development / alpha-tubulin binding / cilium assembly / sperm flagellum / cellular response to unfolded protein / dephosphorylation / sperm midpiece / Hsp70 protein binding / centriole / Neutrophil degranulation / protein-tyrosine-phosphatase / ciliary basal body / mitotic spindle organization / acrosomal vesicle / cellular response to leukemia inhibitory factor / protein tyrosine phosphatase activity / G protein-coupled receptor binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / protein localization / mitochondrial intermembrane space / mitotic spindle / structural constituent of cytoskeleton / cilium / spindle pole / microtubule cytoskeleton organization / SH3 domain binding / intracellular calcium ion homeostasis / calcium-dependent protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.5 Å | ||||||
![]() | Zhu, Y. / Yin, G.L. / Tai, L.H. / Sun, F. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 11.4 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 10.1 MB | Display | ![]() |
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Full document | ![]() | 12.6 MB | Display | |
Data in XML | ![]() | 2 MB | Display | |
Data in CIF | ![]() | 2.8 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35229MC ![]() 8i7rC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() #2: Protein | Mass: 48689.090 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 47897.918 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 50385.066 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 56754.777 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 52121.449 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 23987.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 62817.535 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 36659.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 23097.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 21527.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() 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) ![]() ![]() #15: Protein | Mass: 29587.521 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 16305.608 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 20575.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 176028.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | | Mass: 32786.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #23: Protein | Mass: 27763.268 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #24: Protein | Mass: 19512.373 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() #10: Protein | | Mass: 87758.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() #19: Protein | Mass: 68322.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: Protein | Mass: 22781.389 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 1 types, 123 molecules ![](data/chem/img/GTP.gif)
#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 |
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Sample preparation
Component | Name: mouse sperm / Type: CELL / Entity ID: #1-#24 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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) |
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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 |