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Open data
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Basic information
| Entry | Database: PDB / ID: 9d2f | |||||||||||||||
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| Title | 3D structure and atomic model of RS3 of mouse respiratory cilia | |||||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / axoneme / radial spoke | |||||||||||||||
| Function / homology | Function and homology informationradial spoke stalk / negative regulation of stress granule assembly / diiodophenylpyruvate reductase / pseudophosphatase activity / Malate-aspartate shuttle / positive regulation of hepatic stellate cell migration / positive regulation of hepatic stellate cell contraction / radial spoke assembly / nucleoside-phosphate kinase / (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity ...radial spoke stalk / negative regulation of stress granule assembly / diiodophenylpyruvate reductase / pseudophosphatase activity / Malate-aspartate shuttle / positive regulation of hepatic stellate cell migration / positive regulation of hepatic stellate cell contraction / radial spoke assembly / nucleoside-phosphate kinase / (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity / nucleoside monophosphate kinase activity / regulation of cilium beat frequency / malate dehydrogenase activity / spermatid nucleus elongation / mucociliary clearance / SUMOylation of DNA damage response and repair proteins / sperm flagellum assembly / axonemal central apparatus assembly / radial spoke / Interconversion of nucleotide di- and triphosphates / axonemal dynein complex assembly / vascular associated smooth muscle contraction / inner dynein arm / sperm axoneme assembly / malate-aspartate shuttle / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / XPC complex / inner dynein arm assembly / cerebrospinal fluid circulation / epithelial cilium movement involved in extracellular fluid movement / 9+2 motile cilium / cAMP-dependent protein kinase regulator activity / cilium movement involved in cell motility / Formation of the dystrophin-glycoprotein complex (DGC) / smooth muscle contractile fiber / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / positive regulation of hepatic stellate cell activation / DARPP-32 events / cilium movement / photoreceptor connecting cilium / glomerular mesangial cell development / juxtaglomerular apparatus development / dynein heavy chain binding / PKA activation / motile cilium assembly / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / heterotrimeric G-protein binding / transcription export complex 2 / 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 / adenylate kinase / cilium organization / Smooth Muscle Contraction / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / AURKA Activation by TPX2 / L-malate dehydrogenase (NAD+) activity / Factors involved in megakaryocyte development and platelet production / AMP kinase activity / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / dynein axonemal particle / malate metabolic process / NADP+ metabolic process / nuclear pore nuclear basket / nucleoside-diphosphate kinase / flagellated sperm motility / cell projection organization / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate biosynthetic process / dynein complex / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / microtubule motor activity / minus-end-directed microtubule motor activity / nucleoside diphosphate kinase activity / dynein light intermediate chain binding / motile cilium / cAMP-dependent protein kinase complex / nucleus organization / ciliary base / protein kinase A regulatory subunit binding / mesenchyme migration / protein serine/threonine phosphatase activity / centriole replication / dynein intermediate chain binding / basement membrane / axoneme / mRNA transport / glial cell projection / single fertilization / cellular response to transforming growth factor beta stimulus / sperm flagellum / cAMP binding / intercellular bridge Similarity search - Function | |||||||||||||||
| Biological species | ![]() | |||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||||||||
Authors | Yanhe, Z. / Xuewu, Z. / Daniela, N. | |||||||||||||||
| Funding support | United States, 3items
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Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: Mouse radial spoke 3 is a metabolic and regulatory hub in cilia. Authors: Yanhe Zhao / Kangkang Song / Amirrasoul Tavakoli / Long Gui / Angeles Fernandez-Gonzalez / Song Zhang / Petras P Dzeja / S Alex Mitsialis / Xuewu Zhang / Daniela Nicastro / ![]() Abstract: Cilia are microtubule-based organelles that have important roles in cell sensing, signaling and motility. Recent studies have revealed the atomic structures of many multicomponent ciliary complexes, ...Cilia are microtubule-based organelles that have important roles in cell sensing, signaling and motility. Recent studies have revealed the atomic structures of many multicomponent ciliary complexes, elucidating their mechanisms of action. However, little is known about the structure, proteome and function of full-length radial spoke 3 (RS3), a conserved complex that transmits mechanochemical signals to coordinate ciliary motility. Here, we combined single-particle cryo-electron microscopy, cryo-electron tomography, proteomic analysis and computational modeling to determine the three-dimensional structure and atomic model of RS3 from mouse respiratory cilia. We reveal all RS3 components, including regulatory and metabolic enzymes such as a protein kinase A subunit, adenylate kinases (AKs) and malate dehydrogenases. Furthermore, we confirm RS3 loss in AK7-deficient mice, which exhibit motility defects. Our findings identify RS3 as an important regulatory and metabolic hub that maintains sufficient adenosine triphosphate for sustained ciliary beating, providing insights into the etiology of ciliopathies. | |||||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9d2f.cif.gz | 4.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9d2f.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9d2f.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/9d2f ftp://data.pdbj.org/pub/pdb/validation_reports/d2/9d2f | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 46494MC C: citing same article ( M: map data used to model this data |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-Adenylate kinase ... , 2 types, 3 molecules ADG
| #1: Protein | Mass: 219835.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #24: Protein | Mass: 82643.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 14 types, 17 molecules BCHORPQSILMEFVabc
| #2: Protein | Mass: 39337.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 37712.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 42054.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P62737, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #6: Protein | Mass: 29723.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | | Mass: 19827.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | | Mass: 20105.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | | Mass: 54413.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | | Mass: 41394.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | | Mass: 36555.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P14152, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming), diiodophenylpyruvate reductase #19: Protein | | Mass: 56356.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q5F204, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #20: Protein | | Mass: 10393.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein | | Mass: 58332.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #22: Protein | | Mass: 45442.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #23: Protein | | Mass: 59355.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Cilia- and flagella-associated protein ... , 6 types, 7 molecules NWXYZJK
| #4: Protein | Mass: 91764.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
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| #9: Protein | Mass: 145133.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | | Mass: 193674.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | | Mass: 211839.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | | Mass: 143458.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | | Mass: 148784.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Antibody , 2 types, 2 molecules UT
| #8: Antibody | Mass: 487618.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #12: Antibody | Mass: 475368.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 1 types, 2 molecules 
| #25: Chemical |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | N |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: RS3 from mouse respiratory cilia / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#24 / Source: NATURAL |
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| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 7.4 Details: 30 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA |
| 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 Details: 4 microliters of splayed axoneme sample were applied to glow-discharged Quantifoil R2/2 Cu grids. After removing excess liquid by blotting the grid from the backside with Whatman filter ...Details: 4 microliters of splayed axoneme sample were applied to glow-discharged Quantifoil R2/2 Cu grids. After removing excess liquid by blotting the grid from the backside with Whatman filter paper for 2-3 s, the grid was immediately plunge-frozen in liquid ethane using a home-made plunge freezer. |
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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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Average exposure time: 4.2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 50000 |
| Image scans | Width: 5760 / Height: 4092 |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 280000 Details: particles containing RS3 were manually picked (using the conserved spacing of RSs as guide) centering on the A-tubule of the DMT | ||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63152 Details: The particles used for the head-neck is 37453, the resolution is 7.1. The particle used for the base-stalk is 63152, the resolution is 4.7. Symmetry type: POINT |
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About Yorodumi






United States, 3items
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