[English] 日本語
![](img/lk-miru.gif)
- PDB-3j1t: High affinity dynein microtubule binding domain - tubulin complex -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3j1t | ||||||
---|---|---|---|---|---|---|---|
Title | High affinity dynein microtubule binding domain - tubulin complex | ||||||
![]() |
| ||||||
![]() | MOTOR PROTEIN/STRUCTURAL PROTEIN / MOTOR PROTEIN-STRUCTURAL PROTEIN complex | ||||||
Function / homology | ![]() COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium movement / regulation of metaphase plate congression ...COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium movement / regulation of metaphase plate congression / Resolution of Sister Chromatid Cohesion / establishment of spindle localization / positive regulation of spindle assembly / RHO GTPases Activate Formins / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / manchette / dynein complex / MHC class II antigen presentation / minus-end-directed microtubule motor activity / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / nuclear migration / positive regulation of axon guidance / dynein intermediate chain binding / cytoplasmic microtubule / microtubule-based process / cytoplasmic microtubule organization / stress granule assembly / regulation of mitotic spindle organization / axon cytoplasm / Neutrophil degranulation / mitotic spindle organization / filopodium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nuclear envelope / mitotic cell cycle / nervous system development / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / protein heterodimerization activity / cell division / axon / GTPase activity / centrosome / neuronal cell body / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9.7 Å | ||||||
![]() | Redwine, W.B. / Hernandez-Lopez, R. / Zou, S. / Huang, J. / Reck-Peterson, S.L. / Leschziner, A.E. | ||||||
![]() | ![]() Title: Structural basis for microtubule binding and release by dynein. Authors: W B Redwine / R Hernandez-Lopez / S Zou / J Huang / S L Reck-Peterson / A E Leschziner / ![]() Abstract: Cytoplasmic dynein is a microtubule-based motor required for intracellular transport and cell division. Its movement involves coupling cycles of track binding and release with cycles of force- ...Cytoplasmic dynein is a microtubule-based motor required for intracellular transport and cell division. Its movement involves coupling cycles of track binding and release with cycles of force-generating nucleotide hydrolysis. How this is accomplished given the ~25 nanometers separating dynein's track- and nucleotide-binding sites is not understood. Here, we present a subnanometer-resolution structure of dynein's microtubule-binding domain bound to microtubules by cryo-electron microscopy that was used to generate a pseudo-atomic model of the complex with molecular dynamics. We identified large rearrangements triggered by track binding and specific interactions, confirmed by mutagenesis and single-molecule motility assays, which tune dynein's affinity for microtubules. Our results provide a molecular model for how dynein's binding to microtubules is communicated to the rest of the motor. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 192.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 143.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5439MC ![]() 3j1uC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 18729.609 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 47940.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
Sequence details | CHAINS B AND C ARE DERIVED FROM PDB ENTRY 1JFF. AS A RESULT, THE MODELED SEQUENCES ARE FROM SUS ...CHAINS B AND C ARE DERIVED FROM PDB ENTRY 1JFF. AS A RESULT, THE MODELED SEQUENCES ARE FROM SUS SCROFA (UNP P02550 AND P02554, RESPECTIVE |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-
Sample preparation
Component |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer solution | Name: 50 mM Tris HCl, 1 mM MgCl2, 1mM EGTA, 1mM DTT / pH: 8 / Details: 50 mM Tris HCl, 1 mM MgCl2, 1mM EGTA, 1mM DTT | ||||||||||||||||||||
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: C-flat 2/2-2C holey carbon grids (Protochips) were glow-discharged for 20 seconds at 30 mA in an Edwards carbon evaporator. | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: The solution was blotted manually, and the process of addition and blotting of SRS-MTBD was repeated a total of three times. The final blotting was done inside the humidity chamber of a ...Details: The solution was blotted manually, and the process of addition and blotting of SRS-MTBD was repeated a total of three times. The final blotting was done inside the humidity chamber of a Vitrobot Mark IV (FEI) at 22 Celsius. |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F20 / Date: Apr 10, 2011 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 62000 X / Calibrated magnification: 63377 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.2 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 225 |
-
Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: phase and amplitude correction using Frealign | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -25.76 ° / Axial rise/subunit: 9.26 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Method: Projection matching and back-projection in Fourier space Resolution: 9.7 Å / Num. of particles: 10419 / Nominal pixel size: 1.988 Å / Actual pixel size: 1.988 Å / Magnification calibration: TMV images Details: Projection matching and Helical symmetry operator during reconstruction Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||
Atomic model building | Source name: PDB / Type: experimental model
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST
|