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- PDB-8bwy: In situ outer dynein arm from Chlamydomonas reinhardtii in a pre-... -

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Basic information

Entry
Database: PDB / ID: 8bwy
TitleIn situ outer dynein arm from Chlamydomonas reinhardtii in a pre-power stroke state
Components
  • (Dynein light ...) x 10
  • Calmodulin
  • Docking complex 1/2 protein
  • 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
  • Thioredoxin
KeywordsMOTOR PROTEIN / axoneme / outer dynein arm / pre power stroke / dynein
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 / protein-disulfide reductase activity / microtubule-based process / microtubule ...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 / protein-disulfide reductase activity / microtubule-based process / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
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 / Dynein heavy chain, AAA 5 extension domain ...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 / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 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 / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / 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 / EF-hand domain pair / 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 / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Uncharacterized protein / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein light chain ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Uncharacterized protein / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain / Thioredoxin / Dynein light chain 2A / Dynein heavy chain, outer arm protein / Dynein light chain roadblock-type 2 protein / Dynein light chain / Flagellar outer dynein arm intermediate protein, putative / Dynein light chain
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 38 Å
AuthorsZimmermann, N.E.L. / Noga, A. / Obbineni, J.M. / Ishikawa, T.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationNF310030_192644 Switzerland
Swiss National Science Foundation Switzerland
CitationJournal: EMBO J / Year: 2023
Title: ATP-induced conformational change of axonemal outer dynein arms revealed by cryo-electron tomography.
Authors: Noemi Zimmermann / Akira Noga / Jagan Mohan Obbineni / Takashi Ishikawa /
Abstract: Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram ...Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram averaging, and classification. These states of force generation depict the prepower stroke, postpower stroke, and intermediate state conformations. Comparison of these conformations to published in vitro atomic structures of cytoplasmic dynein, ODA, and the Shulin-ODA complex revealed differences in the orientation and position of the dynein head. Our analysis shows that in the absence of ATP, all dynein linkers interact with the AAA3/AAA4 domains, indicating that interactions with the adjacent microtubule doublet B-tubule direct dynein orientation. For the prepower stroke conformation, there were changes in the tail that is anchored on the A-tubule. We built models starting with available high-resolution structures to generate a best-fitting model structure for the in situ pre- and postpower stroke ODA conformations, thereby showing that ODA in a complex with Shulin adopts a similar conformation as the active prepower stroke ODA in the axoneme.
History
DepositionDec 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
T: Calmodulin
V: Docking complex 1/2 protein
x: Docking complex 1/2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,899,63723
Polymers1,897,84919
Non-polymers1,7894
Water0
1


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

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Components

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Protein , 7 types, 8 molecules ACdePTVx

#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) Chlamydomonas reinhardtii (plant) / 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) Chlamydomonas reinhardtii (plant) / References: UniProt: Q22A67
#4: Protein Dynein intermediate chain 2


Mass: 77888.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: I7M008
#5: 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) Chlamydomonas reinhardtii (plant) / References: UniProt: Q23FU1
#16: Protein Thioredoxin /


Mass: 12855.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q1HFX5
#17: Protein Calmodulin /


Mass: 35237.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: I7M2C6
#18: Protein Docking complex 1/2 protein


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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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) Chlamydomonas reinhardtii (plant) / References: UniProt: I7MHB1
#7: Protein Dynein light chain roadblock-type 2 protein


Mass: 18490.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / 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) Chlamydomonas reinhardtii (plant) / References: UniProt: Q1HFW2
#9: Protein Dynein light chain /


Mass: 12348.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q1HFX0
#10: Protein Dynein light chain /


Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q1HFV9
#11: Protein Dynein light chain /


Mass: 13336.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / 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) Chlamydomonas reinhardtii (plant) / 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) Chlamydomonas reinhardtii (plant) / References: UniProt: Q1HFW0
#14: Protein Dynein light chain 2A


Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / 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) Chlamydomonas reinhardtii (plant) / 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) Chlamydomonas reinhardtii (plant) / References: UniProt: I7M9J2

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Non-polymers , 2 types, 4 molecules

#19: 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
#20: 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

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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: subtomogram averaging

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Sample preparation

ComponentName: In situ outer dynein arm / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3, #6-#18 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 4000 nm
Image recordingElectron dose: 1 e/Å2 / Avg electron dose per subtomogram: 80 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 12 / Num. of volumes extracted: 3553
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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