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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
  • ShulinShulin District
  • Thioredoxin
KeywordsMOTOR PROTEIN / Cilia / dynein / microtubules / motor
Function / homology
Function and homology information


glycerol ether metabolic process / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / cytoskeletal motor activity / protein-disulfide reductase activity / microtubule-based process ...glycerol ether metabolic process / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / cytoskeletal motor activity / protein-disulfide reductase activity / microtubule-based process / cell redox homeostasis / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Uncharacterized protein C20orf194-like / Kelch motif / Galactose oxidase, central domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 ...Uncharacterized protein C20orf194-like / Kelch motif / Galactose oxidase, central domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Roadblock/LAMTOR2 domain / Dynein heavy chain, AAA 5 extension domain / Roadblock/LC7 domain / Dynein heavy chain AAA lid domain / Roadblock/LC7 domain / Dynein heavy chain 3, AAA+ lid domain / Filamin/ABP280 repeat / AAA+ lid domain / Filamin/ABP280 repeat profile. / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Filamin/ABP280 repeat-like / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / 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, 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 / Thioredoxin / IPT/TIG domain / Kelch-type beta propeller / ig-like, plexins, transcription factors / Thioredoxin / IPT domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Immunoglobulin E-set / Thioredoxin-like superfamily / 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 / 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 / Outer arm dynein beta heavy chain / 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 / Outer arm dynein beta heavy chain / 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 / Uncharacterized 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

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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
Water0
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 / Shulin District


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 / Adenosine 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 / Adenosine 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 / Guanosine 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
3ShulinShulin DistrictCOMPLEX#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 FIELDBright-field microscopy
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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