7RRO

Structure of the 48-nm repeat doublet microtubule from bovine tracheal cilia


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

De novo identification of mammalian ciliary motility proteins using cryo-EM.

Gui, M.Farley, H.Anujan, P.Anderson, J.R.Maxwell, D.W.Whitchurch, J.B.Botsch, J.J.Qiu, T.Meleppattu, S.Singh, S.K.Zhang, Q.Thompson, J.Lucas, J.S.Bingle, C.D.Norris, D.P.Roy, S.Brown, A.

(2021) Cell 184: 5791

  • DOI: https://doi.org/10.1016/j.cell.2021.10.007
  • Primary Citation of Related Structures:  
    7RRO

  • PubMed Abstract: 

    Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein C9orf135 homologA [auth 0],
H [auth 7]
232Bos taurusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain family member BB [auth 1],
C [auth 2]
877Bos taurusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-CpG binding domain protein 1D [auth 3],
E [auth 4]
514Bos taurusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase 7F [auth 5],
G [auth 6]
377Bos taurusMutation(s): 0 
EC: 2.7.4.6 (PDB Primary Data), 3.1 (UniProt), 2.7 (UniProt)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C1orf158 homologI [auth 8],
J [auth 9]
196Bos taurusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific nuclear structural protein 1DA [auth B],
K [auth A]
494Bos taurusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-1L [auth A0],
M [auth A1],
N [auth A2],
O [auth A3],
P [auth A4]
418Bos taurusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1D chain452Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-4B chain445Bos taurusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-2430Bos taurusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C1orf189 homologBB [auth C]101Bos taurusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-3490Bos taurusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm associated antigen 8ZB [auth D]484Bos taurusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-4447Bos taurusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 161PD [auth F],
XC [auth E]
321Bos taurusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
TEKTIP1AD [auth E2],
BD [auth E3],
YC [auth E0],
ZC [auth E1]
208Bos taurusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pierce2IE [auth G]120Bos taurusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM166B274Bos taurusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain containing 114XE [auth H1],
YE [auth H2],
ZE [auth H3]
687Bos taurusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Outer dynein arm-docking complex subunit 3AF [auth H4],
BF [auth H5],
CF [auth H6]
621Bos taurusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Armadillo repeat containing 4DF [auth H7],
EF [auth H8],
FF [auth H9]
1,044Bos taurusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
TTC25 proteinVF [auth I1],
WF [auth I2]
683Bos taurusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium-binding domain-containing protein 1XF [auth I3],
YF [auth I4]
212Bos taurusMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A-like with coiled-coils protein 2GJ [auth O],
IK [auth Q],
KL [auth S],
UJ [auth P],
WK [auth R]
377Bos taurusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain containing 1LM [auth U],
YL [auth T],
ZM [auth V]
640Bos taurusMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
EFHC2BO [auth X],
JO [auth Y],
NN [auth W],
QO [auth Z]
733Bos taurusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20193Bos taurusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
PACRG protein257Bos taurusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 45RO [auth a],
SO [auth b],
TO [auth c],
UO [auth d]
549Bos taurusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 52VO [auth e],
WO [auth f],
XO [auth g]
623Bos taurusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Enkurin, TRPC channel interacting proteinAP [auth j],
BP [auth k],
YO [auth h],
ZO [auth i]
259Bos taurusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FlattopCP [auth l],
DP [auth m],
EP [auth n]
196Bos taurusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain containing 173FP [auth o],
GP [auth p]
547Bos taurusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome 3 C1orf194 homologHP [auth q],
IP [auth r],
JP [auth s]
170Bos taurusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
EFCAB6KP [auth t]1,497Bos taurusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Pierce1LP [auth y],
MP [auth z]
136Bos taurusMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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ABA [auth PC]
ACA [auth QG]
ADA [auth RK]
AEA [auth TC]
AGA [auth VM]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

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AAA [auth NJ]
AFA [auth UH]
AS [auth DD]
AX [auth JL]
BQ [auth AJ]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

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AQ [auth AI]
AR [auth BM]
AU [auth FM]
AV [auth HE]
AZ [auth MG]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2021-11-24
    Changes: Database references
  • Version 1.3: 2024-06-05
    Changes: Data collection