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- PDB-6zyw: Outer Dynein Arm-Shulin complex - overall structure (Tetrahymena ... -

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Basic information

Entry
Database: PDB / ID: 6zyw
TitleOuter Dynein Arm-Shulin complex - overall structure (Tetrahymena thermophila)
Components
  • (Dynein light ...) x 10
  • Dynein heavy chain, outer arm protein
  • Dynein intermediate chain 2
  • Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
  • Flagellar outer dynein arm intermediate protein, putative
  • Outer arm dynein beta heavy chain
  • Shulin
  • Thioredoxin
KeywordsMOTOR PROTEIN / Cilia / dynein / microtubules / motor
Function / homology
Function and homology information


axonemal dynein complex / outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding ...axonemal dynein complex / outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / microtubule-based movement / dynein intermediate chain binding / protein-disulfide reductase activity / mRNA transport / microtubule-based process / cell redox homeostasis / protein transport / microtubule / cilium / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Uncharacterized protein C20orf194-like / : / Dynein axonemal assembly factor 9 N-terminal domain / Host cell factor, Kelch-repeats domain / tRNA wybutosine-synthesizing protein 4, beta-propeller / Dynein heavy chain 3, AAA+ lid domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / AAA+ lid domain ...Uncharacterized protein C20orf194-like / : / Dynein axonemal assembly factor 9 N-terminal domain / Host cell factor, Kelch-repeats domain / tRNA wybutosine-synthesizing protein 4, beta-propeller / Dynein heavy chain 3, AAA+ lid domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / AAA+ lid domain / : / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Filamin/ABP280 repeat / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Thioredoxin / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / IPT/TIG domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / ig-like, plexins, transcription factors / Kelch-type beta propeller / IPT domain / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Immunoglobulin E-set / WD domain, G-beta repeat / Thioredoxin-like superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Dynein-1, subspecies f / Dynein light chain / Dynein light chain roadblock-type 2 protein ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Dynein-1, subspecies f / Dynein light chain / Dynein light chain roadblock-type 2 protein / Dynein light chain 2A / Dynein heavy chain, outer arm protein / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein axonemal assembly factor 9 N-terminal domain-containing protein / Flagellar outer dynein arm intermediate protein, putative / Thioredoxin / Dynein light chain / Dynein light chain / Dynein light chain
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.78 Å
AuthorsMali, G.R. / Abid Ali, F. / Lau, C.K. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Science / Year: 2021
Title: Shulin packages axonemal outer dynein arms for ciliary targeting.
Authors: Girish R Mali / Ferdos Abid Ali / Clinton K Lau / Farida Begum / Jérôme Boulanger / Jonathan D Howe / Zhuo A Chen / Juri Rappsilber / Mark Skehel / Andrew P Carter /
Abstract: The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to ...The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to cilia by an unknown mechanism. Here, we used the ciliate to identify two factors (Q22YU3 and Q22MS1) that bind ODAs in the cytoplasm and are required for ODA delivery to cilia. Q22YU3, which we named Shulin, locked the ODA motor domains into a closed conformation and inhibited motor activity. Cryo-electron microscopy revealed how Shulin stabilized this compact form of ODAs by binding to the dynein tails. Our findings provide a molecular explanation for how newly assembled dyneins are packaged for delivery to the cilia.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 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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Structure visualization

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Assembly

Deposited unit
A: Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
B: Outer arm dynein beta heavy chain
C: Dynein heavy chain, outer arm protein
D: Dynein intermediate chain 2
E: Flagellar outer dynein arm intermediate protein, putative
F: Dynein light chain roadblock-type 2 protein
G: Dynein light chain roadblock-type 2 protein
H: Dynein light chain
I: Dynein light chain
J: Dynein light chain
K: Dynein light chain
L: Dynein light chain
M: Dynein light chain
N: Dynein light chain 2A
O: Dynein light chain tctex-type 1 protein
P: Thioredoxin
Y: Shulin
d: Dynein intermediate chain 2
e: Flagellar outer dynein arm intermediate protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,130,90224
Polymers2,128,59019
Non-polymers2,3125
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 8 molecules ACDdEePY

#1: Protein Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative


Mass: 475554.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M6H4
#3: Protein Dynein heavy chain, outer arm protein


Mass: 534328.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22A67
#4: Protein Dynein intermediate chain 2


Mass: 77888.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M008
#5: Protein Flagellar outer dynein arm intermediate protein, putative


Mass: 77178.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23FU1
#16: Protein Thioredoxin


Mass: 12855.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q240X9
#17: Protein Shulin


Mass: 139935.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Shulin
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Strain: SB210 / Gene: TTHERM_00122270 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q22YU3

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Dynein light ... , 10 types, 10 molecules FGHIJKLMNO

#6: Protein Dynein light chain roadblock-type 2 protein


Mass: 14751.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MHB1
#7: Protein Dynein light chain roadblock-type 2 protein


Mass: 11630.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22MV2
#8: Protein Dynein light chain


Mass: 10780.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: A4VE64
#9: Protein Dynein light chain


Mass: 12348.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MCM8
#10: Protein Dynein light chain


Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24DI9
#11: Protein Dynein light chain


Mass: 13336.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22R86
#12: Protein Dynein light chain


Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: W7XJB1
#13: Protein Dynein light chain


Mass: 10453.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24CE5
#14: Protein Dynein light chain 2A


Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q1HGH8
#15: Protein Dynein light chain tctex-type 1 protein


Mass: 13202.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: A4VEB3

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Antibody , 1 types, 1 molecules B

#2: Antibody Outer arm dynein beta heavy chain


Mass: 530182.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M9J2

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Non-polymers , 3 types, 5 molecules

#18: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#19: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#20: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Tetrahymena thermophila ODA Dyh4 motorCOMPLEX#1, #10-#17, #2-#90MULTIPLE SOURCES
2Tetrahymena thermophila ODA Dyh4 motorCOMPLEX#1, #10-#16, #2-#91NATURAL
3ShulinCOMPLEX#171RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Tetrahymena thermophila (strain SB210) (eukaryote)312017
33Tetrahymena thermophila (strain SB210) (eukaryote)312017
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131142 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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