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- PDB-7jts: Stalk of radial spoke 1 attached with doublet microtubule from Ch... -

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Basic information

Entry
Database: PDB / ID: 7jts
TitleStalk of radial spoke 1 attached with doublet microtubule from Chlamydomonas reinhardtii
Components
  • Calmodulin
  • Dynein 8 kDa light chain, flagellar outer arm
  • FAP207
  • FAP253
  • Radial spoke protein 3
KeywordsSTRUCTURAL PROTEIN / cilia / native / complex / microtubule / mechanoregulation
Function / homology
Function and homology information


radial spoke / positive regulation of cilium-dependent cell motility / motile cilium assembly / dynein complex / cytoplasmic dynein complex / ciliary plasm / motile cilium / dynein intermediate chain binding / axoneme / microtubule-based process ...radial spoke / positive regulation of cilium-dependent cell motility / motile cilium assembly / dynein complex / cytoplasmic dynein complex / ciliary plasm / motile cilium / dynein intermediate chain binding / axoneme / microtubule-based process / cilium assembly / enzyme regulator activity / acrosomal vesicle / calcium-mediated signaling / cilium / microtubule / cytoskeleton / calcium ion binding / membrane / cytoplasm
Similarity search - Function
IQ and ubiquitin-like domain-containing protein / Radial spoke 3 / Calmodulin / Radial spoke protein 3 / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / MORN motif / MORN repeat / Dynein light chain type 1 ...IQ and ubiquitin-like domain-containing protein / Radial spoke 3 / Calmodulin / Radial spoke protein 3 / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / MORN motif / MORN repeat / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / IQ motif profile. / IQ motif, EF-hand binding site / EF-hand domain pair / 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
Similarity search - Domain/homology
IQ and ubiquitin-like domain-containing protein / MORN repeat-containing protein 3 / Calmodulin / Uncharacterized protein / Calmodulin / Flagellar radial spoke protein 3 / Dynein 8 kDa light chain, flagellar outer arm
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsGui, M. / Ma, M. / Sze-Tu, E. / Wang, X. / Koh, F. / Zhong, E. / Berger, B. / Davis, J. / Dutcher, S. / Zhang, R. / Brown, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structures of radial spokes and associated complexes important for ciliary motility.
Authors: Miao Gui / Meisheng Ma / Erica Sze-Tu / Xiangli Wang / Fujiet Koh / Ellen D Zhong / Bonnie Berger / Joseph H Davis / Susan K Dutcher / Rui Zhang / Alan Brown /
Abstract: In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two ...In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two complementary cryo-EM strategies to determine structures of the major mechanoregulators that bind ciliary doublet microtubules in Chlamydomonas reinhardtii. We determine structures of isolated radial spoke RS1 and the microtubule-bound RS1, RS2 and the nexin-dynein regulatory complex (N-DRC). From these structures, we identify and build atomic models for 30 proteins, including 23 radial-spoke subunits. We reveal how mechanoregulatory complexes dock to doublet microtubules with regular 96-nm periodicity and communicate with one another. Additionally, we observe a direct and dynamically coupled association between RS2 and the dynein motor inner dynein arm subform c (IDAc), providing a molecular basis for the control of motor activity by mechanical signals. These structures advance our understanding of the role of mechanoregulation in defining the ciliary waveform.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
E: Radial spoke protein 3
F: Radial spoke protein 3
a: Dynein 8 kDa light chain, flagellar outer arm
b: Dynein 8 kDa light chain, flagellar outer arm
c: Dynein 8 kDa light chain, flagellar outer arm
d: Dynein 8 kDa light chain, flagellar outer arm
e: Dynein 8 kDa light chain, flagellar outer arm
f: Dynein 8 kDa light chain, flagellar outer arm
g: Dynein 8 kDa light chain, flagellar outer arm
h: Dynein 8 kDa light chain, flagellar outer arm
m: FAP207
s: FAP253
t: Calmodulin


Theoretical massNumber of molelcules
Total (without water)318,18113
Polymers318,18113
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Radial spoke protein 3


Mass: 56856.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J2J7, UniProt: P12759*PLUS
#2: Protein
Dynein 8 kDa light chain, flagellar outer arm


Mass: 10336.775 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39580
#3: Protein FAP207


Mass: 28418.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DJP7
#4: Protein FAP253


Mass: 75037.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D359
#5: Protein Calmodulin


Mass: 18317.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IDP6, UniProt: P04352*PLUS

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: stalk of radial spoke 1 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-125 / Organelle: cilia
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample is attached with doublet microtubule
Specimen supportDetails: unspecified
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
Image recordingAverage exposure time: 9 sec. / Electron dose: 38.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
5RELION3.1CTF correction
8UCSF Chimeramodel fitting
9Cootmodel fitting
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
14RELION3.13D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143514 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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