[English] 日本語
![](img/lk-miru.gif)
- PDB-3j67: Structural mechanism of the dynein powerstroke (post-powerstroke ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3j67 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural mechanism of the dynein powerstroke (post-powerstroke state) | ||||||
![]() | Dynein motor domain | ||||||
![]() | MOTOR PROTEIN | ||||||
Function / homology | ![]() karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / spindle pole body / dynein intermediate chain binding ...karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / spindle pole body / dynein intermediate chain binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 34 Å | ||||||
![]() | Lin, J. / Okada, K. / Raytchev, M. / Smith, M.C. / Nicastro, D. | ||||||
![]() | ![]() Title: Structural mechanism of the dynein power stroke. Authors: Jianfeng Lin / Kyoko Okada / Milen Raytchev / Maria C Smith / Daniela Nicastro / ![]() Abstract: Dyneins are large microtubule motor proteins required for mitosis, intracellular transport and ciliary and flagellar motility. They generate force through a power-stroke mechanism, which is an ATP- ...Dyneins are large microtubule motor proteins required for mitosis, intracellular transport and ciliary and flagellar motility. They generate force through a power-stroke mechanism, which is an ATP-consuming cycle of pre- and post-power-stroke conformational changes that cause relative motion between different dynein domains. However, key structural details of dynein's force generation remain elusive. Here, using cryo-electron tomography of intact, active (that is, beating), rapidly frozen sea urchin sperm flagella, we determined the in situ three-dimensional structures of all domains of both pre- and post-power-stroke dynein, including the previously unresolved linker and stalk of pre-power-stroke dynein. Our results reveal that the rotation of the head relative to the linker is the key action in dynein movement, and that there are at least two distinct pre-power-stroke conformations: pre-I (microtubule-detached) and pre-II (microtubule-bound). We provide three-dimensional reconstructions of native dyneins in three conformational states, in situ, allowing us to propose a molecular model of the structural cycle underlying dynein movement. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 466.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 370.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5757MC ![]() 5758C ![]() 3j68C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 262122.234 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P36022*PLUS |
---|---|
Sequence details | THE IMAGED DYNEIN WAS FROM STRONGYLOCENTROTUS PURPURATUS, BUT THE MODELED COORDINATES ARE DERIVED ...THE IMAGED DYNEIN WAS FROM STRONGYLOC |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron tomography |
-
Sample preparation
Component | Name: inactive sea urchin sperm flagella / Type: COMPLEX |
---|---|
Buffer solution | pH: 8 Details: 360 mM NaCl, 50 mM MgCl2, 10 mM CaCl2, 10 mM KCl, 30 mM HEPES, pH 8.0, 2 mM erythro-9-[3-(2-hydroxynonyl)]-adenine |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil holey carbon grids Cu 200 mesh R2/2 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: Blot for 1.5-2.5 seconds before plunging in liquid ethane. Method: Blot for 1.5-2.5 seconds before plunging. |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F30 / Date: Apr 28, 2012 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 13500 X / Nominal defocus max: 8000 nm / Nominal defocus min: 6000 nm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: GATAN LIQUID NITROGEN / Temperature: 80 K / Tilt angle max: 65 ° / Tilt angle min: -65 ° |
Image recording | Electron dose: 100 e/Å2 / Film or detector model: GENERIC GATAN (2k x 2k) |
EM imaging optics | Energyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-
Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: fiducial alignment and weighted back-projection / Resolution: 34 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 9.856 Å / Actual pixel size: 9.856 Å Details: Final maps were calculated by averaging 1100 particles from 9 tomograms. 1100 axonemal repeats (96 nm long) from 9 tomograms (reconstructed using fiducial alignment and weighted ...Details: Final maps were calculated by averaging 1100 particles from 9 tomograms. 1100 axonemal repeats (96 nm long) from 9 tomograms (reconstructed using fiducial alignment and weighted backprojection, IMOD software, Kremer et al. 1996) were aligned and averaged using the PEET software (bio3d.colorado.edu, Nicastro et al. 2006). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient Details: REFINEMENT PROTOCOL--rigid body DETAILS--Initial local fitting was done using Chimera and then manual adjustment was performed. | ||||||||||||
Atomic model building | PDB-ID: 4AKI Pdb chain-ID: A / Accession code: 4AKI / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
|