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- PDB-8th8: Linker domain of Nexin-dynein regulatory complex from Tetrahymena... -

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Basic information

Entry
Database: PDB / ID: 8th8
TitleLinker domain of Nexin-dynein regulatory complex from Tetrahymena thermophila
Components
  • (Dynein regulatory complex protein ...) x 3
  • (Growth-arrest-specific microtubule-binding ...) x 2
  • AAA family ATPase CDC48 subfamily protein
  • Calmodulin 7-2
  • Coiled-coil domain-containing protein 153
  • Coiled-coil lobo-like protein, putative
  • Coiled-coil protein, putative
  • DUF4201 domain-containing protein
  • EF-hand calcium-binding domain protein
  • Flagellar associated protein
  • Kinase domain protein
  • LRRC48 protein
KeywordsSTRUCTURAL PROTEIN / nexin-dynein regulatory complex / cilia / axoneme / dynein
Function / homology
Function and homology information


regulation of cilium movement / axonemal dynein complex assembly / sperm axoneme assembly / cytoskeletal motor regulator activity / cilium-dependent cell motility / sperm principal piece / regulation of Arp2/3 complex-mediated actin nucleation / axonemal dynein complex / flagellated sperm motility / actomyosin structure organization ...regulation of cilium movement / axonemal dynein complex assembly / sperm axoneme assembly / cytoskeletal motor regulator activity / cilium-dependent cell motility / sperm principal piece / regulation of Arp2/3 complex-mediated actin nucleation / axonemal dynein complex / flagellated sperm motility / actomyosin structure organization / locomotion / motile cilium / myosin II complex / myosin heavy chain binding / axoneme / mitotic cytokinesis / cilium assembly / sperm flagellum / ciliary basal body / post-embryonic development / cell motility / cilium / small GTPase binding / cell migration / lamellipodium / microtubule binding / microtubule / cytoskeleton / calcium ion binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Coiled-coil domain-containing protein 153 / Dynein regulatory complex subunit 7 / Dynein regulatory complex protein 10 / Domain of unknown function DUF4201 / Dynein regulatory complex protein 9 / Domain of unknown function (DUF4201) / Growth arrest-specific protein 8 domain / Growth arrest-specific protein 8 / Dynein regulatory complex protein 1/2, N-terminal / Dynein regulatory complex protein ...Coiled-coil domain-containing protein 153 / Dynein regulatory complex subunit 7 / Dynein regulatory complex protein 10 / Domain of unknown function DUF4201 / Dynein regulatory complex protein 9 / Domain of unknown function (DUF4201) / 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 / CAP superfamily / EF-hand domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine rich repeat, ribonuclease inhibitor type / 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) / Leucine-rich repeat domain superfamily / ATPase, AAA-type, core / 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 / 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 184 / Calmodulin 7-2 / Dynein regulatory complex subunit 3 / Coiled-coil lobo-like protein, putative / Dynein regulatory complex protein 1/2 N-terminal domain-containing protein / Dynein regulatory complex protein 12 / Dynein regulatory complex protein 9 ...Dynein regulatory complex protein 10 / Growth-arrest-specific microtubule-binding protein / AAA family ATPase CDC48 subfamily protein / Cilia- and flagella-associated protein 184 / Calmodulin 7-2 / Dynein regulatory complex subunit 3 / Coiled-coil lobo-like protein, putative / Dynein regulatory complex protein 1/2 N-terminal domain-containing protein / Dynein regulatory complex protein 12 / Dynein regulatory complex protein 9 / Growth-arrest-specific microtubule-binding protein / Flagellar associated protein / Kinase domain protein / Dynein regulatory complex subunit 2 / EF-hand calcium-binding domain protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsGhanaeian, A.G. / 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 14, 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
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
P: DUF4201 domain-containing protein
Q: Calmodulin 7-2
R: Calmodulin 7-2
S: Coiled-coil domain-containing protein 153
i: EF-hand calcium-binding domain protein
s: Coiled-coil domain-containing protein 153


Theoretical massNumber of molelcules
Total (without water)961,08118
Polymers961,08118
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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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Protein , 10 types, 13 molecules BCFGHIiLPQRSs

#2: Protein Coiled-coil protein, putative


Mass: 60596.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24DJ0
#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
#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
#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 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
#14: 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
#15: 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

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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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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: Linker domain of Nexin-dynein regulatory complex from Tetrahymena thermophila
Type: CELL / Entity ID: #14, #3-#7, #9-#13, #1-#2, #15 / 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 FIELD / 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

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.4 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: 0 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009554178
ELECTRON MICROSCOPYf_angle_d0.615872451
ELECTRON MICROSCOPYf_chiral_restr0.03667760
ELECTRON MICROSCOPYf_plane_restr0.00369485
ELECTRON MICROSCOPYf_dihedral_angle_d4.88156909

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