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- EMDB-46494: 3D structure and atomic structure of RS3 of mouse respiratory cilia -
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Open data
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Basic information
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Title | 3D structure and atomic structure of RS3 of mouse respiratory cilia | ||||||||||||
![]() | 3D structure and atomic model of RS3 of mouse respiratory cilia | ||||||||||||
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![]() | axoneme / radial spoke / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | ![]() radial spoke stalk / positive regulation of hepatic stellate cell migration / positive regulation of hepatic stellate cell contraction / negative regulation of stress granule assembly / pseudophosphatase activity / Malate-aspartate shuttle / diiodophenylpyruvate reductase / radial spoke assembly / nucleoside-phosphate kinase / (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity ...radial spoke stalk / positive regulation of hepatic stellate cell migration / positive regulation of hepatic stellate cell contraction / negative regulation of stress granule assembly / pseudophosphatase activity / Malate-aspartate shuttle / diiodophenylpyruvate reductase / radial spoke assembly / nucleoside-phosphate kinase / (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity / regulation of cilium beat frequency / nucleoside monophosphate kinase activity / inner dynein arm / spermatid nucleus elongation / malate dehydrogenase activity / mucociliary clearance / SUMOylation of DNA damage response and repair proteins / : / axonemal dynein complex assembly / sperm flagellum assembly / axonemal central apparatus assembly / radial spoke / Interconversion of nucleotide di- and triphosphates / vascular associated smooth muscle contraction / sperm axoneme assembly / inner dynein arm assembly / malate-aspartate shuttle / DNA Damage Recognition in GG-NER / XPC complex / Formation of Incision Complex in GG-NER / cerebrospinal fluid circulation / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / cAMP-dependent protein kinase regulator activity / 9+2 motile cilium / positive regulation of hepatic stellate cell activation / smooth muscle contractile fiber / Formation of the dystrophin-glycoprotein complex (DGC) / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / cilium movement / photoreceptor connecting cilium / dynein heavy chain binding / glomerular mesangial cell development / motile cilium assembly / juxtaglomerular apparatus development / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / transcription export complex 2 / heterotrimeric G-protein binding / GPER1 signaling / Hedgehog 'off' state / cilium organization / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Smooth Muscle Contraction / AURKA Activation by TPX2 / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / AMP kinase activity / Factors involved in megakaryocyte development and platelet production / dynein axonemal particle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / malate metabolic process / NADP+ metabolic process / nuclear pore nuclear basket / flagellated sperm motility / nucleoside-diphosphate kinase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / dynein complex / glyceraldehyde-3-phosphate biosynthetic process / minus-end-directed microtubule motor activity / microtubule motor activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / dynein light intermediate chain binding / motile cilium / nucleoside diphosphate kinase activity / cAMP-dependent protein kinase complex / ciliary base / nucleus organization / mesenchyme migration / protein serine/threonine phosphatase activity / dynein intermediate chain binding / centriole replication / basement membrane / axoneme / glial cell projection / mRNA transport / single fertilization / sperm flagellum / cellular response to transforming growth factor beta stimulus / intercellular bridge / cAMP binding / stress fiber Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||
![]() | Yanhe Z / Xuewu Z / Daniela N | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The cryo-EM structure of mouse radial spoke 3 reveals a unique metabolic and regulatory hub in cilia Authors: Yanhe Z / Xuewu Z / Daniela N | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 59.8 KB 59.8 KB | Display Display | ![]() |
Images | ![]() | 19.3 KB | ||
Filedesc metadata | ![]() | 22.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 351.5 KB | Display | ![]() |
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Full document | ![]() | 351.1 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9d2fMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D structure and atomic model of RS3 of mouse respiratory cilia | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.158 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : RS3 from mouse respiratory cilia
+Supramolecule #1: RS3 from mouse respiratory cilia
+Macromolecule #1: Adenylate kinase 9
+Macromolecule #2: Leucine-rich repeat-containing protein 23
+Macromolecule #3: Serine/threonine/tyrosine interacting-like 1
+Macromolecule #4: Cilia- and flagella-associated protein 91
+Macromolecule #5: Actin, aortic smooth muscle
+Macromolecule #6: Axonemal dynein light intermediate polypeptide 1
+Macromolecule #7: Centrin-2
+Macromolecule #8: Dynein axonemal heavy chain 1
+Macromolecule #9: Cilia- and flagella-associated protein 57
+Macromolecule #10: Cilia- and flagella-associated protein 43
+Macromolecule #11: Cilia- and flagella-associated protein 44
+Macromolecule #12: Dynein, axonemal, heavy chain 6
+Macromolecule #13: MORN repeat-containing protein 5
+Macromolecule #14: Cilia- and flagella-associated protein 61
+Macromolecule #15: Cilia- and flagella-associated protein 251
+Macromolecule #16: Tetratricopeptide repeat protein 29
+Macromolecule #17: Zinc finger, MYND domain containing 12
+Macromolecule #18: Malate dehydrogenase, cytoplasmic
+Macromolecule #19: Putative malate dehydrogenase 1B
+Macromolecule #20: UPF0728 protein C10orf53 homolog
+Macromolecule #21: A kinase (PRKA) anchor protein 14
+Macromolecule #22: cAMP-dependent protein kinase type II-alpha regulatory subunit
+Macromolecule #23: Ciliogenesis-associated TTC17-interacting protein
+Macromolecule #24: Adenylate kinase 7
+Macromolecule #25: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Details: 30 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
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
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 50000 / Average exposure time: 4.2 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |