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- EMDB-38020: Radial spoke head-neck dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-38020
TitleRadial spoke head-neck dimer
Map dataRS head-neck dimer composite map
Sample
  • Complex: Radial spoke head-neck dimer
    • Protein or peptide: DPY30 domain containing 2
    • Protein or peptide: DnaJ homolog subfamily B member 13
    • Protein or peptide: Radial spoke head protein 3 homolog B
    • Protein or peptide: Nucleoside diphosphate kinase homolog 5
    • Protein or peptide: Radial spoke head 1 homolog
    • Protein or peptide: Radial spoke head protein 4 homolog A
    • Protein or peptide: Radial spoke head protein 9 homolog
Keywordsradial spoke / cilia / STRUCTURAL PROTEIN
Function / homology
Function and homology information


sperm head-tail coupling apparatus / radial spoke assembly / maintenance of ciliary planar beating movement pattern / radial spoke head 1 / radial spoke head 2 / radial spoke head 3 / axonemal central apparatus assembly / outer dense fiber / radial spoke head / radial spoke ...sperm head-tail coupling apparatus / radial spoke assembly / maintenance of ciliary planar beating movement pattern / radial spoke head 1 / radial spoke head 2 / radial spoke head 3 / axonemal central apparatus assembly / outer dense fiber / radial spoke head / radial spoke / mating / epithelial cilium movement involved in extracellular fluid movement / kinocilium / cilium movement involved in cell motility / 9+2 motile cilium / cilium movement / axoneme assembly / motile cilium 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 / 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 / condensed nuclear chromosome / response to reactive oxygen species / meiotic cell cycle / 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 / : ...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. / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / MORN motif / MORN repeat / Nt-dnaJ domain signature. / DnaJ domain, conserved site / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsMeng X / Cong Y
Funding support China, 1 items
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, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38020.png

Downloads & links

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Map

FileDownload / File: emd_38020.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRS head-neck dimer composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 560 pix.
= 478.24 Å		0.85 Å/pix.
x 560 pix.
= 478.24 Å		0.85 Å/pix.
x 560 pix.
= 478.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.854 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum0.0 - 2.163842
Average (Standard dev.)0.0006550103 (±0.01457182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 478.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Radial spoke head-neck dimer

EntireName: Radial spoke head-neck dimer
Components
  • Complex: Radial spoke head-neck dimer
    • Protein or peptide: DPY30 domain containing 2
    • Protein or peptide: DnaJ homolog subfamily B member 13
    • Protein or peptide: Radial spoke head protein 3 homolog B
    • Protein or peptide: Nucleoside diphosphate kinase homolog 5
    • Protein or peptide: Radial spoke head 1 homolog
    • Protein or peptide: Radial spoke head protein 4 homolog A
    • Protein or peptide: Radial spoke head protein 9 homolog

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Supramolecule #1: Radial spoke head-neck dimer

SupramoleculeName: Radial spoke head-neck dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: DPY30 domain containing 2

MacromoleculeName: DPY30 domain containing 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.235326 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MYPYDVPDYA ENLYFQGAAA MDTAYLKNCF GTGLTQALAE VARVRPSDPI EYLAHWLYHY RSITVAEEKR RQEELQLKEA RDRSAEEAK TTEMLKEEGY QIQQKCEKCH QELPSTSFSS DKTPALQEDT APLEEKTMRQ ESQPGASRVI SEMPQRAIPS

UniProtKB: DPY30 domain containing 2

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Macromolecule #2: DnaJ homolog subfamily B member 13

MacromoleculeName: DnaJ homolog subfamily B member 13 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.119445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKENLYFQG AAAMGLDYYA VLQVTRNSED AQIKKAYRKL ALKNHPLKSS EPGAPEIFKQ IAEAYDVLS DPVKRGIYDK FGEEGLKGGI PLEFGSQTPW TTGYVFHGNP DKVFHEFFGG DNPFSEFFDA EGNDIDLNFG G LWGRGVQK ...String:
MDYKDHDGDY KDHDIDYKDD DDKENLYFQG AAAMGLDYYA VLQVTRNSED AQIKKAYRKL ALKNHPLKSS EPGAPEIFKQ IAEAYDVLS DPVKRGIYDK FGEEGLKGGI PLEFGSQTPW TTGYVFHGNP DKVFHEFFGG DNPFSEFFDA EGNDIDLNFG G LWGRGVQK QDPPIERDLY LSLEDLFFGC TKKIKISRRV LNEDRYSSTI KDKILTIDVR PGWRQGTRIT FEKEGDQGPN II PADIIFI VKEKLHPRFR REHDNLFFVY PIPLGKALTC CTVEVKTLDD RLLNIPINDI VHPKYFKIVP GEGMPLPENP SKK GDLFIF FDIQFPTRLT PQKKQMLRQA LLT

UniProtKB: DnaJ homolog subfamily B member 13

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Macromolecule #3: Radial spoke head protein 3 homolog B

MacromoleculeName: Radial spoke head protein 3 homolog B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 45.23427 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTDRNPRTAE ASGLYTYSSR PRAVACQRRR HRDSILQPVE EPMSYGNIMY DRRVIRGNTY ALPTGQVPGQ PDPLELQRQQ QARRRALAR KRAQEQLKPR TPEPVEGRKH VDIQTELYLE EIADRIVEVD MECQTDAFLD RPPTPLFIPA KTGKDVATQI L GGELFDFD ...String:
MTDRNPRTAE ASGLYTYSSR PRAVACQRRR HRDSILQPVE EPMSYGNIMY DRRVIRGNTY ALPTGQVPGQ PDPLELQRQQ QARRRALAR KRAQEQLKPR TPEPVEGRKH VDIQTELYLE EIADRIVEVD MECQTDAFLD RPPTPLFIPA KTGKDVATQI L GGELFDFD LEVKPMLEVL VGKTIEQSLL EVMEEEELAN LRARQYAYEE IRNVELAEVQ RLEEQERRHR EEKERRKKQQ WE IVHKRNE TLQKISALIF ARQYLANLLP SVFDKLRNSG FFYDPIERDI EVGFLPWLMN EVEKSMEHSM VGRTVLDMLI RDV VERRIN DYEHKEAMPP GQKTNVINGP NTVTDPSVTT LHTQKPVLDR VSSQPAPSQE RKPVEEGGHL MAE

UniProtKB: Radial spoke head protein 3 homolog B

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Macromolecule #4: Nucleoside diphosphate kinase homolog 5

MacromoleculeName: Nucleoside diphosphate kinase homolog 5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.547516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQKLISEED LGSGMEVSMP LPQIYVEKTL ALIKPDVVDK EEEIQDIILG SGFTIIQRRK LHLSPEHCSN FYVEQYGKMF FPNLTAYMS SGPLVAMILA RHKAISYWKE LMGPSNSLVA KETHPDSLRA IYGTDELRNA LHGSNDFAAS EREIRFMFPA V IIEPIPIG ...String:
MEQKLISEED LGSGMEVSMP LPQIYVEKTL ALIKPDVVDK EEEIQDIILG SGFTIIQRRK LHLSPEHCSN FYVEQYGKMF FPNLTAYMS SGPLVAMILA RHKAISYWKE LMGPSNSLVA KETHPDSLRA IYGTDELRNA LHGSNDFAAS EREIRFMFPA V IIEPIPIG QAAKDYINLY VAPTLLQGLT ELCKEKPPDP YLWLADWLMK NNPNKPKLCH FPVTEEP

UniProtKB: Nucleoside diphosphate kinase homolog 5

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Macromolecule #5: Radial spoke head 1 homolog

MacromoleculeName: Radial spoke head 1 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 35.592766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG SGMSDLGSEE LEEEGENDLG EYEGERNEVG ERHGHGKARL PNGDTYEGSY EFGKRHGQGT YKFKNGARYT GDYVKNKKH GQGTFIYPDG SRYEGEWADD QRHGQGVYYY VNNDTYTGEW FNHQRHGQGT YLYAETGSKY VGTWVHGQQE G AAELIHLN ...String:
MWSHPQFEKG SGMSDLGSEE LEEEGENDLG EYEGERNEVG ERHGHGKARL PNGDTYEGSY EFGKRHGQGT YKFKNGARYT GDYVKNKKH GQGTFIYPDG SRYEGEWADD QRHGQGVYYY VNNDTYTGEW FNHQRHGQGT YLYAETGSKY VGTWVHGQQE G AAELIHLN HRYQGKFMNK NPVGPGKYVF DIGCEQHGEY RLTDTERGEE EEEEETLVNI VPKWKALNIT ELALWTPTLS EE QPPPEGQ GQEEPQGLTG VGDPSEDIQA EGFEGELEPR GADEDVDTFR QESQENSYDI DQGNLNFDEE PSDLQD

UniProtKB: Radial spoke head 1 homolog

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Macromolecule #6: Radial spoke head protein 4 homolog A

MacromoleculeName: Radial spoke head protein 4 homolog A / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 80.214102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENSTSLKQE KENQEPGEAE RLWQGESDVS PQEPGPPSPE YREEEQRTDT EPAPRMSPSW SHQSRVSLST GDLTAGPEVS SSPPPPPLQ FHSTPLNTET TQDPVAASPT EKTANGIADT GTPYSDPWES SSAAKQSTSH YTSHAEESTF PQSQTPQPDL C GLRDASRN ...String:
MENSTSLKQE KENQEPGEAE RLWQGESDVS PQEPGPPSPE YREEEQRTDT EPAPRMSPSW SHQSRVSLST GDLTAGPEVS SSPPPPPLQ FHSTPLNTET TQDPVAASPT EKTANGIADT GTPYSDPWES SSAAKQSTSH YTSHAEESTF PQSQTPQPDL C GLRDASRN KSKHKGLRFD LLQEEGSDSN CDPDQPEVGA SEAAQSMLEV AIQNAKAYLL STSSKSGLNL YDHLSKVLTK IL DERPADA VDIIENISQD VKMAHFNKKL DTLHNEYEML PAYEIAETQK ALFLQGHLEG ADSELEEEMA ESSLPNVMES AYY FEQAGV GLGTDETYRV FLALKQLTDT HPIQRCRFWG KILGLEMNYI VAEVEFRDGE DEEEVEEEGI AEERDNGGSE AGEE EEEEL PKSLYKAPQV IPKEESRTGA NKYVYFVCNV PGRPWVRLPS VTPAQIVTAR KIKKFFTGRL DAAVISYPPF PGNES NYLR AQIARISAGT HVSPLGFYQF GEEEGEEEEV EGGRDSYEEN PDFEGIQVID LVESLSNWVH HVQYILPQGR CNWFNP IQK DEDEEEEEEE DEEKGEEPDY IEQEVGPPLL TPISEDLGIQ NIPSWTTQLS SNLIPQYAIA VLRSNLWPGA YAFSNGK KF ENFYIGWGHK YCVENYTPPS PPPVYQEYPS GPEITEMNDP SVEEEQAFRM TQEPVALSTE ENEGTEDEDE DDED

UniProtKB: Radial spoke head protein 4 homolog A

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Macromolecule #7: Radial spoke head protein 9 homolog

MacromoleculeName: Radial spoke head protein 9 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.365902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDADSLLLSL ELASGSGQGL SPDRRASLLT SLMLVKRDYR FARVLFWGRI LGLVADYYIA QGLSEDQLAP RKTLYSLNCT EWSLLPPAT EEMAMQISVV SGRFMGDPSH EYEHTELQKV NEGEKVFDEE VVVQIKEETR LVSIIDQIDK AVAIIPRGAL F KTPFGVTH ...String:
MDADSLLLSL ELASGSGQGL SPDRRASLLT SLMLVKRDYR FARVLFWGRI LGLVADYYIA QGLSEDQLAP RKTLYSLNCT EWSLLPPAT EEMAMQISVV SGRFMGDPSH EYEHTELQKV NEGEKVFDEE VVVQIKEETR LVSIIDQIDK AVAIIPRGAL F KTPFGVTH VNRTFEGLPL SEVRKLSSYF HFREAIDLKN KTLLEKSDLE PSLDFLDSLE YDIPRGSWSI QMERGNALVV LR SLLWPGL TFYHAPRTKN YGYIYVGTGE KNMDLPFML

UniProtKB: Radial spoke head protein 9 homolog

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338084
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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