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Open data
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Basic information
Entry | Database: PDB / ID: 90000000000 | ||||||
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Title | Dimeric motor domains from phi dynein-1 under Lis1 condition | ||||||
![]() | Cytoplasmic dynein 1 heavy chain 1 | ||||||
![]() | MOTOR PROTEIN / dynein-1 / phi | ||||||
Function / homology | ![]() positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / minus-end-directed microtubule motor activity / P-body assembly / dynein light intermediate chain binding ...positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / minus-end-directed microtubule motor activity / P-body assembly / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / stress granule assembly / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / Aggrephagy / Separation of Sister Chromatids / HCMV Early Events / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å | ||||||
![]() | Yang, J. / Zhang, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1. Authors: Jun Yang / Yuanchang Zhao / Pengxin Chai / Ahmet Yildiz / Kai Zhang / ![]() Abstract: Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited ...Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited Phi conformation, a process driven by Lis1 and Nde1/Ndel1. Using biochemical reconstitution and cryo-electron microscopy, we demonstrate that Nde1 enhances Lis1 binding to autoinhibited dynein and facilitates Phi opening. We identify a key intermediate in this activation pathway where a single Lis1 dimer binds between Phi-like (Phi) motor rings. In this 'Phi-Lis1' complex, Lis1 interacts with one motor domain through canonical sites at the AAA+ (adenosine triphosphatases associated with diverse cellular activities) ring and stalk, and with AAA5, AAA6 and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the Phi-Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of Phi-Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 942.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 154.1 KB | Display | |
Data in CIF | ![]() | 236.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 47379MC ![]() 9e0zC ![]() 9e11C ![]() 9e12C ![]() 9e13C ![]() 9e14C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 533083.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ADP / #3: Chemical | #4: Chemical | ChemComp-MG / Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Dimeric motor domains from phi dynein-1 under Lis1 condition Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 1.5 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 Details: 25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 45000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160539 / Symmetry type: POINT |