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- PDB-8x2u: Radial spoke head-neck dimer -

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Basic information

Entry
Database: PDB / ID: 8x2u
TitleRadial spoke head-neck dimer
Components
  • (Radial spoke head protein ...) x 3
  • DPY30 domain containing 2
  • DnaJ homolog subfamily B member 13
  • Nucleoside diphosphate kinase homolog 5
  • Radial spoke head 1 homolog
KeywordsSTRUCTURAL 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 / epithelial cilium movement involved in extracellular fluid movement / kinocilium / cilium movement involved in cell motility / sperm connecting piece / 9+2 motile cilium / cilium movement / motile cilium assembly / axoneme assembly / flagellated sperm motility / ventricular system development / Set1C/COMPASS complex / UTP biosynthetic process / CTP biosynthetic process / motile cilium / meiotic spindle / GTP biosynthetic process / nucleoside diphosphate kinase activity / spermatid development / axoneme / chaperone cofactor-dependent protein refolding / cilium assembly / sperm flagellum / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / 3'-5' exonuclease activity / response to reactive oxygen species / meiotic cell cycle / condensed nuclear chromosome / establishment of localization in cell / cilium / unfolded protein binding / protein-folding chaperone binding / Hydrolases; Acting on ester bonds / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Nucleoside-diphosphate kinase-like NDK-H5 / Radial spokehead-like protein / Radial spoke 3 / Radial spokehead-like protein / Radial spoke protein 3 / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. ...: / Nucleoside-diphosphate kinase-like NDK-H5 / Radial spokehead-like protein / Radial spoke 3 / Radial spokehead-like protein / Radial spoke protein 3 / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / HSP40/DnaJ peptide-binding / MORN repeat / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
DnaJ homolog subfamily B member 13 / Radial spoke head protein 4 homolog A / Radial spoke head 1 homolog / Nucleoside diphosphate kinase homolog 5 / DPY30 domain containing 2 / Radial spoke head protein 9 homolog / Radial spoke head protein 3 homolog B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsMeng, X. / Cong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: 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
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DPY30 domain containing 2
B: DnaJ homolog subfamily B member 13
D: Radial spoke head protein 3 homolog B
E: Nucleoside diphosphate kinase homolog 5
F: Radial spoke head 1 homolog
G: Radial spoke head protein 4 homolog A
H: Radial spoke head protein 9 homolog
I: Radial spoke head 1 homolog
J: Radial spoke head protein 4 homolog A
c: Radial spoke head protein 9 homolog
C: DPY30 domain containing 2
K: DnaJ homolog subfamily B member 13
L: Radial spoke head protein 3 homolog B
M: Nucleoside diphosphate kinase homolog 5
N: Radial spoke head 1 homolog
O: Radial spoke head protein 4 homolog A
P: Radial spoke head protein 9 homolog
Q: Radial spoke head 1 homolog
R: Radial spoke head protein 4 homolog A
d: Radial spoke head protein 9 homolog


Theoretical massNumber of molelcules
Total (without water)846,96420
Polymers846,96420
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 10 molecules ACBKEMFINQ

#1: Protein DPY30 domain containing 2 / Rsph2


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 DnaJ homolog subfamily B member 13 / Rsph16 / Testis and spermatogenesis cell-related protein 6 / Testis spermatocyte apoptosis-related ...Rsph16 / Testis and spermatogenesis cell-related protein 6 / Testis spermatocyte apoptosis-related gene 6 protein / Testis spermatogenesis apoptosis-related gene 3 protein / Testis spermatogenesis apoptosis-related gene 6 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 Nucleoside diphosphate kinase homolog 5 / NDK-H 5 / NDP kinase homolog 5 / Rsph23 / nm23-M5


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
Radial spoke head 1 homolog / Male meiotic metaphase chromosome-associated acidic protein / Meichroacidin / Testis-specific gene A2 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 Radial spoke head protein 3 homolog B / A-kinase anchor protein RSPH3B / Radial spoke head-like protein 2B


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
Radial spoke head protein 4 homolog A / Radial spoke head-like protein 3


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
Radial spoke head protein 9 homolog


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Radial spoke head-neck dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2700 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338084 / Symmetry type: POINT

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