9CPB

Atomic model of bovine Fallopian tube cilia doublet microtubule (48-nm periodicity)

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2024-07-18 Released: 2024-10-30 
  • Deposition Author(s): Zeng, J., Sun, C., Zhang, R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural diversity of axonemes across mammalian motile cilia.

Leung, M.R.Sun, C.Zeng, J.Anderson, J.R.Niu, Q.Huang, W.Noteborn, W.E.M.Brown, A.Zeev-Ben-Mordehai, T.Zhang, R.

(2025) Nature 637: 1170-1177

  • DOI: https://doi.org/10.1038/s41586-024-08337-5
  • Primary Citation of Related Structures:  
    9CPB, 9CPC

  • PubMed Abstract: 

    Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the axoneme is available for the alga Chlamydomonas reinhardtii 1 , structures of mammalian axonemes are incomplete 1-5 . Furthermore, we do not fully understand how molecular structures of axonemes vary across motile-ciliated cell types in the body. Here we use cryoelectron microscopy, cryoelectron tomography and proteomics to resolve the 96-nm modular repeat of axonemal doublet microtubules (DMTs) from both sperm flagella and epithelial cilia of the oviduct, brain ventricles and respiratory tract. We find that sperm DMTs are the most specialized, with epithelial cilia having only minor differences across tissues. We build a model of the mammalian sperm DMT, defining the positions and interactions of 181 proteins including 34 newly identified proteins. We elucidate the composition of radial spoke 3 and uncover binding sites of kinases associated with regeneration of ATP and regulation of ciliary motility. We discover a sperm-specific, axoneme-tethered T-complex protein ring complex (TRiC) chaperone that may contribute to construction or maintenance of the long flagella of mammalian sperm. We resolve axonemal dyneins in their prestroke states, illuminating conformational changes that occur during ciliary movement. Our results illustrate how elements of chemical and mechanical regulation are embedded within the axoneme, providing valuable resources for understanding the aetiology of ciliopathy and infertility, and exemplifying the discovery power of modern structural biology.


  • Organizational Affiliation

    Structural Biochemistry Group, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Armadillo repeat containing 4A [auth 1A]1,044Bos taurusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain containing 114B [auth 1D],
C [auth 1E],
D [auth 1F]
687Bos taurusMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain containing 173E [auth 1H],
F [auth 1I]
547Bos taurusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C1orf158 homologG [auth 1K],
H [auth 1L]
196Bos taurusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FlattopI [auth 1N],
J [auth 1O],
K [auth 1P]
196Bos taurusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP141L [auth 1R]101Bos taurusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 161M [auth 1T],
N [auth 1U]
321Bos taurusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20193Bos taurusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain family member BU [auth 2D],
V [auth 2E]
877Bos taurusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP276W [auth 2F],
X [auth 2G],
Y [auth 2H]
170Bos taurusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 45AA [auth 2K],
BA [auth 2L],
CA [auth 2M],
Z [auth 2J]
549Bos taurusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 52DA [auth 2O],
EA [auth 2P],
FA [auth 2Q]
623Bos taurusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-CpG binding domain protein 1GA [auth 2S],
HA [auth 2T]
514Bos taurusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 77IA [auth 2V],
JA [auth 2W],
KA [auth 2X],
LA [auth 2Y]
284Bos taurusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP95MA [auth 3A]232Bos taurusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia-and flagella-associated protein 96NA [auth 3C],
OA [auth 3D]
309Bos taurusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium-binding domain-containing protein 1PA [auth 3F]212Bos taurusMutation(s): 0 
UniProt
Find proteins for Q32L26 (Bos taurus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium binding domain 6QA [auth 3H]1,410Bos taurusMutation(s): 0 
UniProt
Find proteins for A0AAA9SGY2 (Bos taurus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain containing 1RA [auth 3J],
SA [auth 3K],
TA [auth 3L]
640Bos taurusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
EFHC2UA [auth 3N],
VA [auth 3O],
WA [auth 3P],
XA [auth 3Q]
733Bos taurusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Enkurin, TRPC channel interacting proteinAB [auth 3U],
BB [auth 3V],
YA [auth 3S],
ZA [auth 3T]
259Bos taurusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM166B274Bos taurusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 144IB [auth 4D]135Bos taurusMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific nuclear structural protein 1JB [auth 4F],
KB [auth 4G]
495Bos taurusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase 7LB [auth 4I],
MB [auth 4J]
377Bos taurusMutation(s): 0 
EC: 2.7.4.6 (PDB Primary Data), 3.1 (UniProt), 2.7 (UniProt)
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm-docking complex subunit 3NB [auth 4K],
OB [auth 4L],
PB [auth 4M]
621Bos taurusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
PACRG protein257Bos taurusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pierce1WB [auth 4V],
XB [auth 4W]
136Bos taurusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Pierce2YB [auth 4Y]120Bos taurusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A-like with coiled-coils protein 2AC [auth 5B],
ZB [auth 5A]
377Bos taurusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm acrosome associated 9169Bos taurusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-1IC [auth 5L],
JC [auth 5M],
KC [auth 5N],
LC [auth 5O]
418Bos taurusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-2430Bos taurusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-3490Bos taurusMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-4447Bos taurusMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
TTC25 proteinQD [auth 6Y],
RD [auth 6Z]
683Bos taurusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ciliary microtubule associated protein 1ASD [auth 7C],
TD [auth 7D],
UD [auth 7E],
VD [auth 7F]
254Bos taurusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ciliary microtubule associated protein 1CWD [auth 7H],
XD [auth 7I]
274Bos taurusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 90YD [auth 7K],
ZD [auth 7L]
147Bos taurusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm associated antigen 8AE [auth 7N]484Bos taurusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-4B chain445Bos taurusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1D chain452Bos taurusMutation(s): 0 
EC: 3.6.5
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
ABA [auth UM]
AQ [auth CM]
AR [auth EM]
BR [auth FC]
BS [auth GI]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
AAA [auth TF]
AS [auth GH]
AU [auth JH]
AV [auth KN]
AW [auth MH]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
ACA [auth WG]
AP [auth BE]
AT [auth HM]
AX [auth NK]
BAA [auth TF]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

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 States1R01 GM138854

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Data collection, Database references
  • Version 1.2: 2025-02-12
    Changes: Data collection, Database references