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Yorodumi- PDB-8bwy: In situ outer dynein arm from Chlamydomonas reinhardtii in a pre-... -
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-Basic information
Entry | Database: PDB / ID: 8bwy | |||||||||
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Title | In situ outer dynein arm from Chlamydomonas reinhardtii in a pre-power stroke state | |||||||||
Components |
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Keywords | MOTOR PROTEIN / axoneme / outer dynein arm / pre 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 / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex ...outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / protein-disulfide reductase activity / microtubule / centrosome / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 38 Å | |||||||||
Authors | Zimmermann, N.E.L. / Noga, A. / Obbineni, J.M. / Ishikawa, T. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bwy.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8bwy.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 8bwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bwy_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8bwy_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8bwy_validation.xml.gz | 312.9 KB | Display | |
Data in CIF | 8bwy_validation.cif.gz | 522.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwy ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwy | HTTPS FTP |
-Related structure data
Related structure data | 16304MC 8bx8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 7 types, 8 molecules ACdePTVx
#1: Protein | Mass: 475554.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: I7M6H4 |
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#3: 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 | 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 | 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 | 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 | 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 | Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) |
-Dynein light ... , 10 types, 10 molecules FGHIJKLMNO
#6: Protein | Mass: 14751.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: I7MHB1 |
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#7: 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | Mass: 13202.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A4VEB3 |
-Antibody , 1 types, 1 molecules B
#2: Antibody | 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 | #20: Chemical | ChemComp-ATP / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: In situ outer dynein arm / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3, #6-#18 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 4000 nm |
Image recording | Electron dose: 1 e/Å2 / Avg electron dose per subtomogram: 80 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package |
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CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 12 / Num. of volumes extracted: 3553 |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |