+Open data
-Basic information
Entry | Database: PDB / ID: 8x2u | ||||||
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Title | Radial spoke head-neck dimer | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / radial spoke / cilia | ||||||
Function / homology | Function and homology information radial spoke head 1 / radial spoke head 2 / radial spoke head 3 / radial spoke assembly / maintenance of ciliary planar beating movement pattern / outer dense fiber / axonemal central apparatus assembly / radial spoke head / radial spoke / mating ...radial spoke head 1 / radial spoke head 2 / radial spoke head 3 / radial spoke assembly / maintenance of ciliary planar beating movement pattern / outer dense fiber / axonemal central apparatus assembly / radial spoke head / radial spoke / mating / kinocilium / cilium movement involved in cell motility / epithelial cilium movement involved in extracellular fluid movement / : / 9+2 motile cilium / cilium movement / motile cilium assembly / axoneme assembly / flagellated sperm motility / ventricular system development / Set1C/COMPASS complex / CTP biosynthetic process / UTP biosynthetic process / motile cilium / meiotic spindle / GTP biosynthetic process / nucleoside diphosphate kinase activity / axoneme / chaperone cofactor-dependent protein refolding / spermatid development / cilium assembly / sperm flagellum / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / 3'-5' exonuclease activity / meiotic cell cycle / condensed nuclear chromosome / establishment of localization in cell / response to reactive oxygen species / cilium / unfolded protein binding / protein-folding chaperone binding / Hydrolases; Acting on ester bonds / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å | ||||||
Authors | Meng, X. / Cong, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Multi-scale structures of the mammalian radial spoke and divergence of axonemal complexes in ependymal cilia. Authors: Xueming Meng / Cong Xu / Jiawei Li / Benhua Qiu / Jiajun Luo / Qin Hong / Yujie Tong / Chuyu Fang / Yanyan Feng / Rui Ma / Xiangyi Shi / Cheng Lin / Chen Pan / Xueliang Zhu / Xiumin Yan / Yao Cong / Abstract: Radial spokes (RS) transmit mechanochemical signals between the central pair (CP) and axonemal dynein arms to coordinate ciliary motility. Atomic-resolution structures of metazoan RS and structures ...Radial spokes (RS) transmit mechanochemical signals between the central pair (CP) and axonemal dynein arms to coordinate ciliary motility. Atomic-resolution structures of metazoan RS and structures of axonemal complexes in ependymal cilia, whose rhythmic beating drives the circulation of cerebrospinal fluid, however, remain obscure. Here, we present near-atomic resolution cryo-EM structures of mouse RS head-neck complex in both monomer and dimer forms and reveal the intrinsic flexibility of the dimer. We also map the genetic mutations related to primary ciliary dyskinesia and asthenospermia on the head-neck complex. Moreover, we present the cryo-ET and sub-tomogram averaging map of mouse ependymal cilia and build the models for RS1-3, IDAs, and N-DRC. Contrary to the conserved RS structure, our cryo-ET map reveals the lack of IDA-b/c/e and the absence of Tektin filaments within the A-tubule of doublet microtubules in ependymal cilia compared with mammalian respiratory cilia and sperm flagella, further exemplifying the structural diversity of mammalian motile cilia. Our findings shed light on the stepwise mammalian RS assembly mechanism, the coordinated rigid and elastic RS-CP interaction modes beneficial for the regulation of asymmetric ciliary beating, and also facilitate understanding on the etiology of ciliary dyskinesia-related ciliopathies and on the ependymal cilia in the development of hydrocephalus. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x2u.cif.gz | 793.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x2u.ent.gz | 618.4 KB | Display | PDB format |
PDBx/mmJSON format | 8x2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x2u_validation.pdf.gz | 850.4 KB | Display | wwPDB validaton report |
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Full document | 8x2u_full_validation.pdf.gz | 880 KB | Display | |
Data in XML | 8x2u_validation.xml.gz | 106.3 KB | Display | |
Data in CIF | 8x2u_validation.cif.gz | 164.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/8x2u ftp://data.pdbj.org/pub/pdb/validation_reports/x2/8x2u | HTTPS FTP |
-Related structure data
Related structure data | 38020MC 8wzbC 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 , 4 types, 10 molecules ACBKEMFINQ
#1: Protein | Mass: 18235.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dydc2 / Production host: Homo sapiens (human) / References: UniProt: Q9D3X8 #2: Protein | Mass: 40119.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnajb13, Tsarg, Tsarg3, Tsarg6 / Production host: Homo sapiens (human) / References: UniProt: Q80Y75 #4: Protein | Mass: 25547.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nme5 / Production host: Homo sapiens (human) / References: UniProt: Q99MH5 #5: Protein | Mass: 35592.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rsph1, Tsga2 / Production host: Homo sapiens (human) / References: UniProt: Q8VIG3 |
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-Radial spoke head protein ... , 3 types, 10 molecules DLGJORHcPd
#3: Protein | Mass: 45234.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rsph3b, Rshl2, Rshl2b / Production host: Homo sapiens (human) / References: UniProt: Q9DA80 #6: Protein | Mass: 80214.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rsph4a, Rshl3 / Production host: Homo sapiens (human) / References: UniProt: Q8BYM7 #7: Protein | Mass: 31365.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rsph9 / Production host: Homo sapiens (human) / References: UniProt: Q9D9V4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Radial spoke head-neck dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338084 / Symmetry type: POINT |