9CPC

Atomic model of porcine brain ventricles cilia doublet microtubule (48-nm periodicity)

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2024-07-18 Released: 2024-10-23 
  • 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: 3.65 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 protein 4 isoform 1A [auth 1A],
B [auth 1B]
1,048Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm-docking complex subunit 4C [auth 1C],
D [auth 1D]
685Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium binding domain 1E [auth 1F],
F [auth 1G]
262Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 114 isoform X2G [auth 1H],
H [auth 1I],
I [auth 1J]
711Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm docking complex subunit 3J [auth 1L],
K [auth 1M],
L [auth 1N]
620Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0VZV9 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
EFCAB6M [auth 1P],
N [auth 1Q]
1,456Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1CPW5 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 52O [auth 1S],
P [auth 1T],
Q [auth 1U]
620Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 45R [auth 1W],
S [auth 1X],
T [auth 1Y],
U [auth 1Z]
549Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 210V [auth 2B],
W [auth 2C]
552Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 276X [auth 2E],
Y [auth 2F],
Z [auth 2G]
170Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
EnkurinAA [auth 2I],
BA [auth 2J],
CA [auth 2K]
256Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Parkin coregulated257Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20JA [auth 2T],
KA [auth 2U],
LA [auth 2V],
MA [auth 2W],
NA [auth 2X]
193Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FlattopOA [auth 3A],
PA [auth 3B],
QA [auth 3C]
177Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
TektinRA [auth 3E],
SA [auth 3F],
TA [auth 3G],
UA [auth 3H]
418Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
TektinVA [auth 3J],
WA [auth 3K],
XA [auth 3L],
YA [auth 3M]
430Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
TektinAB [auth 3P],
BB [auth 3Q],
CB [auth 3R],
ZA [auth 3O]
490Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
TektinDB [auth 3T],
EB [auth 3U],
FB [auth 3V],
GB [auth 3W]
447Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A domain with coiled-coils 2HB [auth 3Y],
IB [auth 3Z]
377Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A-like with coiled-coils protein 1JB [auth 4A],
KB [auth 4B]
379Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain containing 1LB [auth 4D],
MB [auth 4E],
NB [auth 4F]
640Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing family member C2OB [auth 4H],
PB [auth 4I],
QB [auth 4J],
RB [auth 4K]
748Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ciliary microtubule inner protein 2BSB [auth 4M],
TB [auth 4N],
VB [auth 4P],
WB [auth 4Q],
XB [auth 4R]
272Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ciliary microtubule inner protein 2BUB [auth 4O]252Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-associated antigen 8 isoform 1YB [auth 4T]469Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase homolog 7AC [auth 4W],
ZB [auth 4V]
377Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 161BC [auth 4Y],
CC [auth 4Z]
314Sus scrofaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome 1 C9orf135 homologDC [auth 5B]230Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Piercer of microtubule wall 1EC [auth 5D],
FC [auth 5E]
136Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome 1 C15orf65 homologGC [auth 5G]121Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain family member BHC [auth 5I],
IC [auth 5J]
879Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 141JC [auth 5L]101Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific nuclear structural protein 1KC [auth 5N],
LC [auth 5O]
495Sus scrofaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 53MC [auth 5Q],
NC [auth 5R]
514Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP107/C1orf158OC [auth 5T],
PC [auth 5U]
196Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 77QC [auth 5W],
RC [auth 5X],
SC [auth 5Y],
TC [auth 5Z]
282Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 144UC [auth 6A]135Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia-and flagella-associated protein 96VC [auth 6C],
WC [auth 6D]
310Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm acrosome associated 9223Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chain447Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2QX54 (Sus scrofa)
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Go to UniProtKB:  A0A5G2QX54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5G2QX54
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain449Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2QGK1 (Sus scrofa)
Explore A0A5G2QGK1 
Go to UniProtKB:  A0A5G2QGK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5G2QGK1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
AO [auth BF]
AP [auth DG]
AQ [auth FN]
AS [auth KB]
AT [auth MH]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
AR [auth HP]
AV [auth QN]
AX [auth VB]
BQ [auth FN]
BR [auth HQ]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 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: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection
  • Version 1.2: 2025-01-08
    Changes: Data collection, Database references
  • Version 1.3: 2025-02-12
    Changes: Data collection, Database references