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- PDB-6zyx: Outer Dynein Arm-Shulin complex - Shulin region from Tetrahymena ... -

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Basic information

Entry
Database: PDB / ID: 6zyx
TitleOuter Dynein Arm-Shulin complex - Shulin region from Tetrahymena thermophila
Components
  • (Dynein light ...) x 6
  • Dynein heavy chain, outer arm protein
  • Dynein intermediate chain 2
  • Flagellar outer dynein arm intermediate protein, putative
  • ShulinShulin District
KeywordsMOTOR PROTEIN / Cilia / Microtubules / Motor / Complex
Function / homology
Function and homology information


dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Uncharacterized protein C20orf194-like / 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 / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain ...Uncharacterized protein C20orf194-like / 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 / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Dynein light chain 2A / Dynein heavy chain, outer arm protein / Dynein light chain / Uncharacterized protein / Flagellar outer dynein arm intermediate protein, putative / Dynein light chain / Dynein light chain / Dynein light chain
Similarity search - Component
Biological speciesTetrahymena thermophila CU428 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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 1.1Feb 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 17, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4May 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
C: Dynein heavy chain, outer arm protein
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
Y: Shulin
d: Dynein intermediate chain 2
e: Flagellar outer dynein arm intermediate protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)905,94411
Polymers905,42110
Non-polymers5231
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28100 Å2
ΔGint-122 kcal/mol
Surface area105420 Å2
MethodPISA

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Components

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Protein , 4 types, 4 molecules CYde

#1: 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 CU428 (eukaryote) / References: UniProt: Q22A67
#8: Protein Shulin / Shulin District


Mass: 139935.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila CU428 (eukaryote)
Gene: TTHERM_00122270 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q22YU3
#9: Protein Dynein intermediate chain 2


Mass: 77888.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: I7M008
#10: Protein Flagellar outer dynein arm intermediate protein, putative


Mass: 77178.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q23FU1

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Dynein light ... , 6 types, 6 molecules JKLMNO

#2: Protein Dynein light chain /


Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q24DI9
#3: Protein Dynein light chain /


Mass: 13336.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q22R86
#4: Protein Dynein light chain /


Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: W7XJB1
#5: Protein Dynein light chain /


Mass: 10453.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q24CE5
#6: Protein Dynein light chain 2A


Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q1HGH8
#7: 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 CU428 (eukaryote) / References: UniProt: A4VEB3

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Non-polymers , 1 types, 1 molecules

#11: 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
1Shulin region from Outer Dynein Arm-Shulin complex (Tetrahymena thermophila). Contains Shulin (excluding C3 finger), Lc8e, Lc8f, Lc8d, Lc8, Lc2a, Lc9, Dic N-termini and portion of Dyh3 tail.COMPLEX#1-#100MULTIPLE SOURCES
2DyneinCOMPLEX#1-#7, #9-#101NATURAL
3ShulinShulin DistrictCOMPLEX#81RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Tetrahymena thermophila CU428 (eukaryote)452467
23Tetrahymena thermophila CU428 (eukaryote)452467
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
VitrificationCryogen name: ETHANE

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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

SoftwareName: PHENIX / Version: dev_3965: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43338 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00917060
ELECTRON MICROSCOPYf_angle_d1.03923000
ELECTRON MICROSCOPYf_dihedral_angle_d15.6446353
ELECTRON MICROSCOPYf_chiral_restr0.0542524
ELECTRON MICROSCOPYf_plane_restr0.0062922

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