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- PDB-7kzo: Outer dynein arm docking complex bound to doublet microtubules fr... -

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Basic information

Entry
Database: PDB / ID: 7kzo
TitleOuter dynein arm docking complex bound to doublet microtubules from C. reinhardtii
Components
  • (Outer dynein arm-docking complex ...) x 2
  • Dynein gamma chain, flagellar outer arm
  • Outer dynein arm protein 1
  • Tubulin alpha
  • Tubulin beta
KeywordsMOTOR PROTEIN / dynein / microtubule / cilia
Function / homology
Function and homology information


outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton ...outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / ODAD1 central coiled coil region / 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 ...: / ODAD1 central coiled coil region / 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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Outer dynein arm protein 1 / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Dynein gamma chain, flagellar outer arm / Outer dynein arm-docking complex protein DC3
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWalton, T. / Wu, H. / Brown, A.B.
CitationJournal: Nat Commun / Year: 2021
Title: Structure of a microtubule-bound axonemal dynein.
Authors: Travis Walton / Hao Wu / Alan Brown /
Abstract: Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily ...Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 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.identifier_ORCID / _citation_author.name
Revision 1.2Mar 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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Structure visualization

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Assembly

Deposited unit
A1: Tubulin beta
A2: Tubulin alpha
A3: Tubulin beta
A4: Tubulin alpha
A5: Tubulin beta
A6: Tubulin alpha
A7: Tubulin beta
B1: Tubulin beta
B2: Tubulin alpha
B3: Tubulin beta
B4: Tubulin alpha
B5: Tubulin beta
B6: Tubulin alpha
B7: Tubulin beta
C: Dynein gamma chain, flagellar outer arm
X: Outer dynein arm-docking complex subunit 1
Y: Outer dynein arm protein 1
X1: Outer dynein arm-docking complex subunit 1
Y1: Outer dynein arm protein 1
Z: Outer dynein arm-docking complex protein DC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,529,01642
Polymers1,521,63820
Non-polymers7,37822
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area79680 Å2
ΔGint-412 kcal/mol
Surface area256960 Å2

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Components

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Protein , 4 types, 17 molecules A1A3A5A7B1B3B5B7A2A4A6B2B4B6CYY1

#1: Protein
Tubulin beta / Tubulin beta-1/beta-2 chain / Beta-tubulin


Mass: 49665.809 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P04690
#2: Protein
Tubulin alpha / Tubulin alpha-1 chain


Mass: 49638.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09204
#3: Protein Dynein gamma chain, flagellar outer arm


Mass: 513491.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39575
#5: Protein Outer dynein arm protein 1 / Docking complex component 2


Mass: 62292.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF70

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Outer dynein arm-docking complex ... , 2 types, 3 molecules XX1Z

#4: Protein Outer dynein arm-docking complex subunit 1


Mass: 83518.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A8IPZ5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#6: Protein Outer dynein arm-docking complex protein DC3 / Outer dynein arm-docking complex subunit 3


Mass: 21371.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7Y0H2

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Non-polymers , 3 types, 22 molecules

#7: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, 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: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ODA docking complex / Type: COMPLEX
Details: ODA-DC bound to doublet microtubules showing contacts with the N-terminal tail of heavy chain gamma
Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.4
Details: Buffer also contained 1x Protease Arrest (G-Biosciences)
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMHEPES1
225 mMKCl1
35 mMMgSO41
40.5 mMEGTA1
510 mMATPAdenosine triphosphate1
60.75 mMCaCl21
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Splayed axonemes isolated from Chlamydomonas reinhardtii flagella.
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples ...Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples were prepared by first blotting for 10 s with blot force set to 16 and immediately plunged into liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.7 sec. / Electron dose: 61.48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 20524
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Coot0.9.1model fitting
9PHENIX1.18.2model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 82 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 5584147
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 485694
Details: The composite map was generated from three focused refinements of the full ODA-DC map. The three focused refinements centered on DC1/2 (3.1 A), DC3 (3.2 A), and heavy chain gamma (3.2 A).
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation coefficient

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