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- PDB-8tid: Combined linker domain of N-DRC and associated proteins Tetrahymena -

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Entry
Database: PDB / ID: 8tid
TitleCombined linker domain of N-DRC and associated proteins Tetrahymena
Components
  • (Coiled-coil protein, ...Coiled coil) x 2
  • (Dynein regulatory complex protein ...) x 3
  • (Flagellar associated ...) x 2
  • (Growth-arrest-specific microtubule-binding ...) x 2
  • (WD40 domain protein) x 2
  • AAA family ATPase CDC48 subfamily protein
  • CFAP20
  • Calmodulin 7-2
  • Cilia- and flagella-associated protein 91
  • Coiled-coil domain-containing protein 153
  • Coiled-coil lobo-like protein, putative
  • DUF4201 domain-containing protein
  • EF hand protein
  • EF-hand calcium-binding domain protein
  • Flagella associated protein
  • Kinase domain protein
  • L-shape (Unknown-protein)
  • LRRC48 protein
KeywordsSTRUCTURAL PROTEIN / nexin-dynein regulatory complex / cilia / axoneme / dynein
Function / homology
Function and homology information


axonemal dynein complex / axonemal dynein complex assembly / inner dynein arm assembly / cilium movement / axoneme assembly / motile cilium / axoneme / cell projection / cell motility / cilium ...axonemal dynein complex / axonemal dynein complex assembly / inner dynein arm assembly / cilium movement / axoneme assembly / motile cilium / axoneme / cell projection / cell motility / cilium / small GTPase binding / microtubule binding / microtubule / cytoskeleton / calcium ion binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Coiled-coil domain-containing protein 153 / Dynein regulatory complex subunit 7 / Dynein regulatory complex protein 10 / Cilia- and flagella-associated protein 91 / CFAP91 domain / Coiled-coil domain-containing protein 39 / Coiled-coil domain-containing protein 40 / Dynein regulatory complex protein 9 / Cilia- and flagella-associated protein 91 / Growth arrest-specific protein 8 domain ...Coiled-coil domain-containing protein 153 / Dynein regulatory complex subunit 7 / Dynein regulatory complex protein 10 / Cilia- and flagella-associated protein 91 / CFAP91 domain / Coiled-coil domain-containing protein 39 / Coiled-coil domain-containing protein 40 / Dynein regulatory complex protein 9 / Cilia- and flagella-associated protein 91 / Growth arrest-specific protein 8 domain / Growth arrest-specific protein 8 / Dynein regulatory complex protein 1/2, N-terminal / Dynein regulatory complex protein / Growth-arrest specific micro-tubule binding / Sperm tail / BRE1 E3 ubiquitin ligase / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / EF-hand domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine Rich repeat / Leucine-rich repeat, SDS22-like subfamily / IQ motif profile. / IQ motif, EF-hand binding site / Leucine-rich repeat profile. / Leucine-rich repeat / Papain-like cysteine peptidase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Leucine-rich repeat domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein regulatory complex protein 10 / Growth-arrest-specific microtubule-binding protein / AAA family ATPase CDC48 subfamily protein / Cilia- and flagella-associated protein 91 / Cilia- and flagella-associated protein 184 / Calmodulin 7-2 / Dynein regulatory complex subunit 3 / Coiled-coil lobo-like protein, putative / EF hand protein / Dynein regulatory complex protein 1/2 N-terminal domain-containing protein ...Dynein regulatory complex protein 10 / Growth-arrest-specific microtubule-binding protein / AAA family ATPase CDC48 subfamily protein / Cilia- and flagella-associated protein 91 / Cilia- and flagella-associated protein 184 / Calmodulin 7-2 / Dynein regulatory complex subunit 3 / Coiled-coil lobo-like protein, putative / EF hand protein / Dynein regulatory complex protein 1/2 N-terminal domain-containing protein / Cilia- and flagella-associated protein 263 / Cilia- and flagella-associated protein 20 / Coiled-coil domain-containing protein 153 / Coiled-coil protein, putative / WD40 domain protein / Flagella associated protein / Dynein regulatory complex protein 9 / Growth-arrest-specific microtubule-binding protein / Flagellar associated protein / Kinase domain protein / Dynein regulatory complex subunit 2 / WD40 domain protein / EF-hand calcium-binding domain protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGhanaeian, A.G. / Majhi, S.M. / McCaffrey, C.M. / Nami, B.N. / Black, C.B. / Yang, S.K. / Legal, T.L. / Papoulas, O.P. / Janowska, M.J. / Valente-Paterno, M.V. ...Ghanaeian, A.G. / Majhi, S.M. / McCaffrey, C.M. / Nami, B.N. / Black, C.B. / Yang, S.K. / Legal, T.L. / Papoulas, O.P. / Janowska, M.J. / Valente-Paterno, M.V. / Marcotte, E.M. / Wloga, D.W. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2023
Title: Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism.
Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward ...Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui /
Abstract: Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein ...Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein regulatory complex (N-DRC), which links adjacent doublet microtubules and regulates and coordinates the activity of outer doublet complexes. Despite its critical role in cilia motility, the assembly and molecular basis of the regulatory mechanism are poorly understood. Here, using cryo-electron microscopy in conjunction with biochemical cross-linking and integrative modeling, we localize 12 DRC subunits in the N-DRC structure of Tetrahymena thermophila. We also find that the CCDC96/113 complex is in close contact with the DRC9/10 in the linker region. In addition, we reveal that the N-DRC is associated with a network of coiled-coil proteins that most likely mediates N-DRC regulatory activity.
History
DepositionJul 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein regulatory complex protein 1/2 N-terminal domain-containing protein
B: Coiled-coil protein, putative
C: LRRC48 protein
D: Growth-arrest-specific microtubule-binding protein
E: Growth-arrest-specific microtubule-binding protein
F: Flagellar associated protein
G: Kinase domain protein
H: Coiled-coil lobo-like protein, putative
I: EF-hand calcium-binding domain protein
J: Dynein regulatory complex protein 9
K: Dynein regulatory complex protein 10
L: AAA family ATPase CDC48 subfamily protein
M: Cilia- and flagella-associated protein 91
N: Flagella associated protein
O: Coiled-coil protein, putative
P: DUF4201 domain-containing protein
Q: Calmodulin 7-2
R: Calmodulin 7-2
S: Coiled-coil domain-containing protein 153
T: Flagellar associated protein
U: L-shape (Unknown-protein)
V: L-shape (Unknown-protein)
W: WD40 domain protein
Z: EF hand protein
g: CFAP20
i: EF-hand calcium-binding domain protein
n: Flagella associated protein
o: Coiled-coil protein, putative
s: Coiled-coil domain-containing protein 153
w: WD40 domain protein


Theoretical massNumber of molelcules
Total (without water)2,072,90530
Polymers2,072,90530
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Dynein regulatory complex protein ... , 3 types, 3 molecules AJK

#1: Protein Dynein regulatory complex protein 1/2 N-terminal domain-containing protein


Mass: 98840.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q229S1
#10: Protein Dynein regulatory complex protein 9


Mass: 44990.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23S05
#11: Protein Dynein regulatory complex protein 10


Mass: 51315.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VD15

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Coiled-coil protein, ... , 2 types, 3 molecules BOo

#2: Protein Coiled-coil protein, putative / Coiled coil


Mass: 60596.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24DJ0
#15: Protein Coiled-coil protein, putative / Coiled coil


Mass: 105196.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q233L0

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Protein , 15 types, 20 molecules CGHIiLMNnPQRSsUVWZgw

#3: Protein LRRC48 protein


Mass: 68009.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MG46
#7: Protein Kinase domain protein


Mass: 39706.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24CL2
#8: Protein Coiled-coil lobo-like protein, putative


Mass: 101225.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLZ4
#9: Protein EF-hand calcium-binding domain protein


Mass: 22062.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7WX86
#12: Protein AAA family ATPase CDC48 subfamily protein


Mass: 101144.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LWE3
#13: Protein Cilia- and flagella-associated protein 91


Mass: 76154.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LWP7
#14: Protein Flagella associated protein


Mass: 114163.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23BW0
#16: Protein DUF4201 domain-containing protein


Mass: 94540.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M6D6
#17: Protein Calmodulin 7-2


Mass: 23862.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MDA9
#18: Protein Coiled-coil domain-containing protein 153


Mass: 22170.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22RH5
#20: Protein L-shape (Unknown-protein)


Mass: 50825.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#21: Protein WD40 domain protein


Mass: 151719.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7WWA2
#22: Protein EF hand protein /


Mass: 124971.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MM07
#23: Protein CFAP20 / Transcription factor iib protein / putative


Mass: 22976.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22NU3
#24: Protein WD40 domain protein


Mass: 152700.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q234G8

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Growth-arrest-specific microtubule-binding ... , 2 types, 2 molecules DE

#4: Protein Growth-arrest-specific microtubule-binding protein


Mass: 56190.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LT80
#5: Protein Growth-arrest-specific microtubule-binding protein


Mass: 55393.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23YW7

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Flagellar associated ... , 2 types, 2 molecules FT

#6: Protein Flagellar associated protein


Mass: 52938.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24C31
#19: Protein Flagellar associated protein


Mass: 42931.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22KK0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Combined linker domain of N-DRC and associated proteins Tetrahymena
Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: OTHER / Num. of particles: 211502 / Symmetry type: POINT

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