9D2F | pdb_00009d2f

3D structure and atomic model of RS3 of mouse respiratory cilia

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2024-08-08 Released: 2025-08-13 
  • Deposition Author(s): Yanhe, Z., Xuewu, Z., Daniela, N.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mouse radial spoke 3 is a metabolic and regulatory hub in cilia.

Zhao, Y.Song, K.Tavakoli, A.Gui, L.Fernandez-Gonzalez, A.Zhang, S.Dzeja, P.P.Mitsialis, S.A.Zhang, X.Nicastro, D.

(2025) Nat Struct Mol Biol 32: 1542-1554

  • DOI: https://doi.org/10.1038/s41594-025-01594-6
  • Primary Citation of Related Structures:  
    9D2F

  • PubMed Abstract: 

    Cilia are microtubule-based organelles that have important roles in cell sensing, signaling and motility. Recent studies have revealed the atomic structures of many multicomponent ciliary complexes, elucidating their mechanisms of action. However, little is known about the structure, proteome and function of full-length radial spoke 3 (RS3), a conserved complex that transmits mechanochemical signals to coordinate ciliary motility. Here, we combined single-particle cryo-electron microscopy, cryo-electron tomography, proteomic analysis and computational modeling to determine the three-dimensional structure and atomic model of RS3 from mouse respiratory cilia. We reveal all RS3 components, including regulatory and metabolic enzymes such as a protein kinase A subunit, adenylate kinases (AKs) and malate dehydrogenases. Furthermore, we confirm RS3 loss in AK7-deficient mice, which exhibit motility defects. Our findings identify RS3 as an important regulatory and metabolic hub that maintains sufficient adenosine triphosphate for sustained ciliary beating, providing insights into the etiology of ciliopathies.


  • Organizational Affiliation
    • Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylate kinase 91,894Mus musculusMutation(s): 0 
EC: 2.7.4.3 (PDB Primary Data), 2.7.4.4 (UniProt), 2.7.4.6 (UniProt)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing protein 23
B, C
340Mus musculusMutation(s): 0 
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IMPC:  MGI:1315192
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine/tyrosine interacting-like 1D [auth H]321Mus musculusMutation(s): 0 
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IMPC:  MGI:1923821
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UniProt GroupQ9DAR2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 91E [auth N]783Mus musculusMutation(s): 0 
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IMPC:  MGI:2443598
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, aortic smooth muscleF [auth O],
I [auth R]
377Mus musculusMutation(s): 0 
EC: 3.6.4
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IMPC:  MGI:87909
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Axonemal dynein light intermediate polypeptide 1G [auth P],
H [auth Q]
258Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Centrin-2J [auth S]172Mus musculusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein axonemal heavy chain 1K [auth U]4,250Mus musculusMutation(s): 0 
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IMPC:  MGI:107721
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 57L [auth W],
M [auth X]
1,249Mus musculusMutation(s): 0 
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IMPC:  MGI:2686209
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 43N [auth Y]1,682Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 44O [auth Z]1,843Mus musculusMutation(s): 0 
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IMPC:  MGI:1277238
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein, axonemal, heavy chain 6P [auth T]4,144Mus musculusMutation(s): 0 
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IMPC:  MGI:107744
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
MORN repeat-containing protein 5Q [auth I]170Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 61R [auth J]1,252Mus musculusMutation(s): 0 
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IMPC:  MGI:1926024
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 251S [auth K]1,299Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Tetratricopeptide repeat protein 29T [auth L]471Mus musculusMutation(s): 0 
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IMPC:  MGI:1920551
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger, MYND domain containing 12U [auth M]363Mus musculusMutation(s): 0 
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IMPC:  MGI:2140259
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase, cytoplasmicV [auth E]334Mus musculusMutation(s): 0 
EC: 1.1.1.37 (PDB Primary Data), 1.1.1.96 (PDB Primary Data)
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IMPC:  MGI:97051
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative malate dehydrogenase 1BW [auth F]500Mus musculusMutation(s): 0 
EC: 1.1.1
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IMPC:  MGI:1923918
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0728 protein C10orf53 homologX [auth V]93Mus musculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
A kinase (PRKA) anchor protein 14Y [auth a]536Mus musculusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase type II-alpha regulatory subunitZ [auth b]401Mus musculusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ciliogenesis-associated TTC17-interacting proteinAA [auth c]520Mus musculusMutation(s): 0 
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IMPC:  MGI:2685062
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylate kinase 7BA [auth D],
CA [auth G]
723Mus musculusMutation(s): 0 
EC: 2.7.4.3 (PDB Primary Data), 2.7.4.6 (UniProt)
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IMPC:  MGI:1926051
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM083122
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR140082
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM130289

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Data collection, Database references