[English] 日本語
Yorodumi
- PDB-8bx8: In situ outer dynein arm from Chlamydomonas reinhardtii in the po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bx8
TitleIn situ outer dynein arm from Chlamydomonas reinhardtii in the post-power stroke state
Components
  • (Dynein light ...) x 12
  • 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 / post power stroke / dynein
Function / homology
Function and homology information


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 ...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 / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / microtubule / calcium ion binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kelch motif / Dynein light chain Tctex-1 like / Dynein heavy chain 3, AAA+ lid domain / Tctex-1-like superfamily / Tctex-1 family / Galactose oxidase, central domain / : / AAA+ lid domain / : / Dynein light chain, type 1/2 ...Kelch motif / Dynein light chain Tctex-1 like / Dynein heavy chain 3, AAA+ lid domain / Tctex-1-like superfamily / Tctex-1 family / Galactose oxidase, central domain / : / AAA+ lid domain / : / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / 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, 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 / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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 / EF hand / IPT/TIG domain / Kelch-type beta propeller / ig-like, plexins, transcription factors / Leucine-rich repeat, SDS22-like subfamily / Thioredoxin / IPT domain / : / Leucine-rich repeat profile. / Thioredoxin domain / Leucine-rich repeat / EF-hand domain pair / Leucine-rich repeat domain superfamily / 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 / Immunoglobulin E-set / Thioredoxin-like superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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 / Thioredoxin / 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 roadblock-type 2 protein / Dynein light chain / Dynein light chain ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Thioredoxin / 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 roadblock-type 2 protein / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain 4A / Dynein light chain 2A / Dynein light chain 1 / Dynein heavy chain, outer arm protein / Dynein light chain roadblock-type 2 protein / Flagellar outer dynein arm intermediate protein, putative / Dynein light chain
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 30.3 Å
AuthorsZimmermann, N.E.L. / Noga, A. / Obbineni, J.M. / Ishikawa, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationNF310030_192644 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 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynein heavy chain, outer arm protein
B: Outer arm dynein beta heavy chain
C: Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
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 tctex-type 1 protein
O: Dynein light chain 2A
P: Thioredoxin
Q: Dynein light chain 1
R: Dynein light chain 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,883,79636
Polymers1,879,49218
Non-polymers4,30318
Water00
1


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

-
Components

-
Protein , 5 types, 5 molecules ACDEP

#1: Protein Dynein heavy chain, outer arm protein


Mass: 534400.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22A67
#3: 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 (eukaryote) / References: UniProt: I7M6H4
#4: Protein Dynein intermediate chain 2


Mass: 76685.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / 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) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23FU1
#16: Protein Thioredoxin


Mass: 14256.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VD75

-
Dynein light ... , 12 types, 12 molecules FGHIJKLMNOQR

#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 (eukaryote) / 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) Tetrahymena thermophila (eukaryote) / 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 (eukaryote) / 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) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFX0
#10: Protein Dynein light chain


Mass: 11435.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#11: Protein Dynein light chain


Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFV9
#12: Protein Dynein light chain


Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / 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 (eukaryote) / References: UniProt: Q1HFW0
#14: 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 (eukaryote) / References: UniProt: A4VEB3
#15: Protein Dynein light chain 2A


Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HGH8
#17: Protein Dynein light chain 1


Mass: 22851.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HGH9
#18: Protein Dynein light chain 4A


Mass: 17822.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFX4

-
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 (eukaryote) / References: UniProt: I7M9J2

-
Non-polymers , 3 types, 18 molecules

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


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#20: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#21: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: In situ outer dynein arm / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#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

-
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 FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 3000 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)

-
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: 30.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2131 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 8 / Num. of volumes extracted: 3167
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more