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- PDB-8tek: Baseplate of Nexin-dynein regulatory complex from Tetrahymena the... -

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Basic information

Entry
Database: PDB / ID: 8tek
TitleBaseplate of Nexin-dynein regulatory complex from Tetrahymena thermophila
Components
  • (Coiled-coil protein, ...Coiled coil) x 2
  • (Growth-arrest-specific microtubule-binding ...) x 2
  • CFAP20
  • Cilia- and flagella-associated protein 91
  • DUF4201 domain-containing protein
  • Dynein regulatory complex protein 1/2 N-terminal domain-containing protein
  • Flagella associated protein
  • Flagellar associated protein
KeywordsPROTEIN BINDING / complex / Cilia / axoneme / nexin-dynein regulatory complex
Function / homology
Function and homology information


axonemal dynein complex assembly / inner dynein arm assembly / cilium movement / axoneme assembly / axonemal dynein complex / motile cilium / axoneme / cell projection / cell motility / cilium ...axonemal dynein complex assembly / inner dynein arm assembly / cilium movement / axoneme assembly / axonemal dynein complex / motile cilium / axoneme / cell projection / cell motility / cilium / small GTPase binding / microtubule binding / microtubule / cytoskeleton / cytoplasm
Similarity search - Function
Cilia- and flagella-associated protein 91 / CFAP91 domain / Coiled-coil domain-containing protein 39 / Coiled-coil domain-containing protein 40 / 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 ...Cilia- and flagella-associated protein 91 / CFAP91 domain / Coiled-coil domain-containing protein 39 / Coiled-coil domain-containing protein 40 / 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
Similarity search - Domain/homology
Growth-arrest-specific microtubule-binding protein / Cilia- and flagella-associated protein 91 / Cilia- and flagella-associated protein 184 / 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 protein, putative / Flagella associated protein / Growth-arrest-specific microtubule-binding protein / Dynein regulatory complex subunit 2
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGhanaeian, A.G. / Black, C.S. / Yang, S.K. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04774 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 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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
D: Growth-arrest-specific microtubule-binding protein
E: Growth-arrest-specific microtubule-binding protein
M: Cilia- and flagella-associated protein 91
N: Flagella associated protein
O: Coiled-coil protein, putative
P: DUF4201 domain-containing protein
T: Flagellar associated protein
g: CFAP20


Theoretical massNumber of molelcules
Total (without water)726,98310
Polymers726,98310
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, cross-linking, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules AMNPTg

#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 / Details: The baseplate domain of the DRC1 / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q229S1
#5: 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
#6: Protein Flagella associated protein


Mass: 114163.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23BW0
#8: 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
#9: 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
#10: 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

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Coiled-coil protein, ... , 2 types, 2 molecules BO

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


Mass: 60596.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The baseplate domain of the DRC2 / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24DJ0
#7: Protein Coiled-coil protein, putative / Coiled coil


Mass: 105196.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q233L0

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

#3: 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
#4: 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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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: Baseplate of Nexin-dynein regulatory complex from Tetrahymena thermophila
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Single Particle Analysis of baseplate domain of Nexin-Dynein regulatory complex of Tetrahymena thermophila
Entity ID: #8-#9, #1-#7, #10 / 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
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 7.78 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01515422
ELECTRON MICROSCOPYf_angle_d0.601320583
ELECTRON MICROSCOPYf_chiral_restr0.03932269
ELECTRON MICROSCOPYf_plane_restr0.00412643
ELECTRON MICROSCOPYf_dihedral_angle_d5.3161960

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