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Yorodumi- PDB-8iyj: Cryo-EM structure of the 48-nm repeat doublet microtubule from mo... -
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-Basic information
Entry | Database: PDB / ID: 8iyj | ||||||
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Title | Cryo-EM structure of the 48-nm repeat doublet microtubule from mouse sperm | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / doublet microtubule | ||||||
Function / homology | Function and homology information male germ-line stem cell population maintenance / protein localization to motile cilium / outer dense fiber / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / 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 / outer dense fiber / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / 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 / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / positive regulation of feeding behavior / cerebrospinal fluid circulation / 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 / 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 / cilium movement / protein localization to organelle / Aggrephagy / Transferases; Transferring phosphorus-containing groups / 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 / sperm DNA condensation / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / cilium organization / Recycling pathway of L1 / axonemal microtubule / left/right axis specification / COPI-dependent Golgi-to-ER retrograde traffic / gamma-tubulin ring complex / 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 / positive regulation of cilium assembly / negative regulation of TOR signaling / MHC class II antigen presentation / protein targeting to mitochondrion / nucleotide-activated protein kinase complex / 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 / myosin phosphatase activity / extrinsic component of membrane / intercellular bridge / beta-tubulin binding / protein-serine/threonine phosphatase / receptor clustering / regulation of neuron projection development / AMP binding / regulation of cell division / single fertilization / axoneme / phosphatase activity / spermatid development / cerebral cortex cell migration / mitotic cytokinesis / alpha-tubulin binding / centriolar satellite / cilium assembly / cellular response to UV-C Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zhou, L.N. / Gui, M. / Wu, J.P. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell / Year: 2023 Title: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iyj.cif.gz | 34.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8iyj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8iyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iyj ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iyj | HTTPS FTP |
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-Related structure data
Related structure data | 35823MC 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
-Cilia- and flagella-associated protein ... , 12 types, 33 molecules 07348AN1EFN2I1L1XAXBXCXDXEXFXGXHaa6bcdefgop...
#1: Protein | Mass: 26633.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC3 #3: 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 #5: 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 #6: Protein | Mass: 12278.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9D9 #15: Protein | Mass: 34433.383 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8Y0 #18: Protein | | Mass: 19552.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D131 #21: Protein | | Mass: 20886.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAR0 #35: Protein | Mass: 22781.389 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BTU1 #39: Protein | Mass: 65962.016 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9U9 #42: 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 #47: 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 #48: Protein | Mass: 18960.092 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAD0 |
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-EF-hand domain-containing family member ... , 2 types, 6 molecules 12WXYZ
#2: 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 #31: Protein | Mass: 87758.023 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D485 |
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+Protein , 29 types, 521 molecules 56j1A0A1A2A3A4A5AAACAEAGAIAKAMAOBCBEBGBIBKBMBOCCCECGCICKCM...
-Piercer of microtubule wall ... , 2 types, 2 molecules Gy
#16: 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 |
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#49: 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 |
-RIB43A-like with coiled-coils protein ... , 2 types, 5 molecules OPQRS
#23: Protein | Mass: 45032.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0B8 #29: Protein | Mass: 45328.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4Q1 |
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-Testis-expressed ... , 2 types, 9 molecules P3P4P5P6P7h1h2h3h4
#27: Protein | Mass: 21069.139 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAG4 #44: Protein | Mass: 16305.608 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9I1 |
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-Non-polymers , 3 types, 532 molecules
#50: Chemical | ChemComp-GTP / #51: Chemical | ChemComp-MG / #52: Chemical | ChemComp-GDP / |
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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: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mouse sperm DMT / Type: COMPLEX / Entity ID: #1-#49 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1500 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.56 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 25135 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: phenix.real_space_refine / Classification: refinement |
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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: 95290 / Symmetry type: POINT |