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- PDB-9d2f: 3D structure and atomic model of RS3 of mouse respiratory cilia -

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Basic information

Entry
Database: PDB / ID: 9d2f
Title3D structure and atomic model of RS3 of mouse respiratory cilia
Components
  • (Adenylate kinase ...) x 2
  • (Cilia- and flagella-associated protein ...) x 6
  • A kinase (PRKA) anchor protein 14
  • Actin, aortic smooth muscle
  • Axonemal dynein light intermediate polypeptide 1
  • Centrin-2
  • Ciliogenesis-associated TTC17-interacting protein
  • Dynein axonemal heavy chain 1
  • Dynein, axonemal, heavy chain 6
  • Leucine-rich repeat-containing protein 23
  • MORN repeat-containing protein 5
  • Malate dehydrogenase, cytoplasmic
  • Putative malate dehydrogenase 1B
  • Serine/threonine/tyrosine interacting-like 1
  • Tetratricopeptide repeat protein 29
  • UPF0728 protein C10orf53 homolog
  • Zinc finger, MYND domain containing 12
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsSTRUCTURAL PROTEIN / axoneme / radial spoke
Function / homology
Function and homology information


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
A-kinase anchor protein 28kDa / Uncharacterised protein family UPF0728 / : / 28 kDa A-kinase anchor / Uncharacterised protein family UPF0728 / MORN repeat-containing protein 5 / : / : / : / Ciliogenesis-associated TTC17-interacting protein, N-terminal domain ...A-kinase anchor protein 28kDa / Uncharacterised protein family UPF0728 / : / 28 kDa A-kinase anchor / Uncharacterised protein family UPF0728 / MORN repeat-containing protein 5 / : / : / : / Ciliogenesis-associated TTC17-interacting protein, N-terminal domain / : / CFAP61 dimerisation domain / : / Echinoderm microtubule-associated protein second beta-propeller / Cilia- and flagella-associated protein 61, N-terminal domain / Cilia- and flagella-associated protein 61 / Cilia- and flagella-associated protein 61, N-terminal domain / Malate dehydrogenase, NAD-dependent, cytosolic / : / : / Axonemal dynein light chain / Axonemal dynein light chain / : / Echinoderm microtubule-associated protein first beta-propeller / Cilia- and flagella-associated protein 91 / CFAP91 domain / : / Cilia- and flagella-associated protein 91 / Malate dehydrogenase, type 2 / Dpy-30 motif / Dpy-30 motif / Dynein heavy chain 3, AAA+ lid domain / : / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / AAA+ lid domain / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / : / : / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / MORN motif / MORN repeat / Adenylate kinase/UMP-CMP kinase / Quinoprotein amine dehydrogenase, beta chain-like / Adenylate kinase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Leucine-rich repeat / Rhodanese-like domain superfamily / Tetratricopeptide repeat / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Rhodanese-like domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Leucine Rich repeat / L-lactate/malate dehydrogenase / Cyclic nucleotide-binding domain signature 2. / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Cyclic nucleotide-binding domain signature 1. / ATP-dependent RNA helicase DEAD-box, conserved site / Cyclic nucleotide-binding, conserved site / Leucine-rich repeat, SDS22-like subfamily
Similarity search - Domain/homology
Zinc finger, MYND domain containing 12 / Ciliogenesis-associated TTC17-interacting protein / Dynein, axonemal, heavy chain 6 / Cilia- and flagella-associated protein 44 / Cilia- and flagella-associated protein 251 / Cilia- and flagella-associated protein 43 / Dynein axonemal heavy chain 1 / Tetratricopeptide repeat protein 29 / Adenylate kinase 7 / Adenylate kinase 9 ...Zinc finger, MYND domain containing 12 / Ciliogenesis-associated TTC17-interacting protein / Dynein, axonemal, heavy chain 6 / Cilia- and flagella-associated protein 44 / Cilia- and flagella-associated protein 251 / Cilia- and flagella-associated protein 43 / Dynein axonemal heavy chain 1 / Tetratricopeptide repeat protein 29 / Adenylate kinase 7 / Adenylate kinase 9 / Leucine-rich repeat-containing protein 23 / cAMP-dependent protein kinase type II-alpha regulatory subunit / Malate dehydrogenase, cytoplasmic / Actin, aortic smooth muscle / UPF0728 protein C10orf53 homolog / A kinase (PRKA) anchor protein 14 / Putative malate dehydrogenase 1B / Cilia- and flagella-associated protein 91 / Axonemal dynein light intermediate polypeptide 1 / Cilia- and flagella-associated protein 61 / Cilia- and flagella-associated protein 57 / MORN repeat-containing protein 5 / Serine/threonine/tyrosine interacting-like 1 / Centrin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsYanhe, Z. / Xuewu, Z. / Daniela, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM083122 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140082 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
CitationJournal: To Be Published
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
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase 9
B: Leucine-rich repeat-containing protein 23
C: Leucine-rich repeat-containing protein 23
H: Serine/threonine/tyrosine interacting-like 1
N: Cilia- and flagella-associated protein 91
O: Actin, aortic smooth muscle
P: Axonemal dynein light intermediate polypeptide 1
Q: Axonemal dynein light intermediate polypeptide 1
R: Actin, aortic smooth muscle
S: Centrin-2
U: Dynein axonemal heavy chain 1
W: Cilia- and flagella-associated protein 57
X: Cilia- and flagella-associated protein 57
Y: Cilia- and flagella-associated protein 43
Z: Cilia- and flagella-associated protein 44
T: Dynein, axonemal, heavy chain 6
I: MORN repeat-containing protein 5
J: Cilia- and flagella-associated protein 61
K: Cilia- and flagella-associated protein 251
L: Tetratricopeptide repeat protein 29
M: Zinc finger, MYND domain containing 12
E: Malate dehydrogenase, cytoplasmic
F: Putative malate dehydrogenase 1B
V: UPF0728 protein C10orf53 homolog
a: A kinase (PRKA) anchor protein 14
b: cAMP-dependent protein kinase type II-alpha regulatory subunit
c: Ciliogenesis-associated TTC17-interacting protein
D: Adenylate kinase 7
G: Adenylate kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,090,15331
Polymers3,090,02229
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Adenylate kinase ... , 2 types, 3 molecules ADG

#1: Protein Adenylate kinase 9


Mass: 219835.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G3UYQ4, adenylate kinase
#24: Protein Adenylate kinase 7


Mass: 82643.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: F8WIC0, adenylate kinase

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Protein , 14 types, 17 molecules BCHORPQSILMEFVabc

#2: Protein Leucine-rich repeat-containing protein 23 / Leucine-rich protein B7


Mass: 39337.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35125
#3: Protein Serine/threonine/tyrosine interacting-like 1 / Styxl1 protein


Mass: 37712.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAR2
#5: Protein Actin, aortic smooth muscle / Alpha-actin-2


Mass: 42054.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P62737, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#6: Protein Axonemal dynein light intermediate polypeptide 1 / Inner dynein arm light chain / axonemal


Mass: 29723.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BVN8
#7: Protein Centrin-2 / Caltractin isoform 1


Mass: 19827.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1K9
#13: Protein MORN repeat-containing protein 5


Mass: 20105.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAI9
#16: Protein Tetratricopeptide repeat protein 29


Mass: 54413.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9QLU4
#17: Protein Zinc finger, MYND domain containing 12


Mass: 41394.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2BGJ5
#18: Protein Malate dehydrogenase, cytoplasmic / Aromatic alpha-keto acid reductase / KAR / Cytosolic malate dehydrogenase


Mass: 36555.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P14152, malate dehydrogenase, diiodophenylpyruvate reductase
#19: Protein Putative malate dehydrogenase 1B


Mass: 56356.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q5F204, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#20: Protein UPF0728 protein C10orf53 homolog


Mass: 10393.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3KNL4
#21: Protein A kinase (PRKA) anchor protein 14


Mass: 58332.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3V0I7
#22: Protein cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 45442.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12367
#23: Protein Ciliogenesis-associated TTC17-interacting protein


Mass: 59355.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: B9EKE5

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Cilia- and flagella-associated protein ... , 6 types, 7 molecules NWXYZJK

#4: Protein Cilia- and flagella-associated protein 91 / CFAP91 / AMY-1-associating protein expressed in testis 1 homolog / AAT-1 / MYCBP/AMY-1-associated ...CFAP91 / AMY-1-associating protein expressed in testis 1 homolog / AAT-1 / MYCBP/AMY-1-associated testis-expressed protein 1 / Protein MAATS1


Mass: 91764.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BRC6
#9: Protein Cilia- and flagella-associated protein 57 / WD repeat-containing protein 65


Mass: 145133.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D180
#10: Protein Cilia- and flagella-associated protein 43


Mass: 193674.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q7R9
#11: Protein Cilia- and flagella-associated protein 44


Mass: 211839.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q5M6
#14: Protein Cilia- and flagella-associated protein 61


Mass: 143458.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8CEL2
#15: Protein Cilia- and flagella-associated protein 251 / WD repeat-containing protein 66


Mass: 148784.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q743

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Antibody , 2 types, 2 molecules UT

#8: Antibody Dynein axonemal heavy chain 1 / Axonemal beta dynein heavy chain 1 / Ciliary dynein heavy chain 1 / mDHC7


Mass: 487618.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q8T7
#12: Antibody Dynein, axonemal, heavy chain 6


Mass: 475368.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q0B6

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Non-polymers , 1 types, 2 molecules

#25: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: RS3 from mouse respiratory cilia / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#24 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
Details: 30 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
4cryoSPARC3.3.1CTF correction
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. 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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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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