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Open data
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Basic information
Entry | Database: PDB / ID: 8pqy | ||||||||||||
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Title | Cytoplasmic dynein-1 motor domain bound to LIS1 | ||||||||||||
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![]() | MOTOR PROTEIN / Dynein / AAA-Atpase / p150 / LIS1 | ||||||||||||
Function / homology | ![]() corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / platelet activating factor metabolic process / radial glia-guided pyramidal neuron migration ...corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / platelet activating factor metabolic process / radial glia-guided pyramidal neuron migration / cerebral cortex neuron differentiation / microtubule organizing center organization / positive regulation of intracellular transport / central region of growth cone / acrosome assembly / positive regulation of embryonic development / reelin-mediated signaling pathway / regulation of metaphase plate congression / establishment of centrosome localization / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / establishment of spindle localization / astral microtubule / axonemal dynein complex / positive regulation of spindle assembly / nuclear membrane disassembly / layer formation in cerebral cortex / auditory receptor cell development / vesicle transport along microtubule / positive regulation of dendritic spine morphogenesis / stem cell division / stereocilium / myeloid leukocyte migration / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / P-body assembly / negative regulation of JNK cascade / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule plus-end binding / cytoplasmic dynein complex / brain morphogenesis / motile cilium / retrograde axonal transport / nuclear migration / microtubule associated complex / osteoclast development / kinesin complex / dynein intermediate chain binding / dynein complex binding / cochlea development / cell leading edge / transmission of nerve impulse / germ cell development / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule-based process / dynactin binding / phospholipase binding / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / lipid catabolic process / regulation of microtubule cytoskeleton organization / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cytoplasmic microtubule organization / regulation of mitotic spindle organization / JNK cascade / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / adult locomotory behavior / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / hippocampus development / phosphoprotein binding / neuron migration / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cerebral cortex development / kinetochore / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Singh, K. / Lau, C.K. / Manigrasso, G. / Gassmann, R. / Carter, A.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1. Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter / ![]() ![]() Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 662.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 103.2 KB | Display | |
Data in CIF | ![]() | 158 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17828MC ![]() 8pqvC ![]() 8pqwC ![]() 8pqzC ![]() 8pr0C ![]() 8pr1C ![]() 8pr2C ![]() 8pr3C ![]() 8pr4C ![]() 8pr5C ![]() 8ptkC 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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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 533055.125 Da / Num. of mol.: 1 / Mutation: R1567E, K1610E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Protein | Mass: 46709.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ATP / | Has ligand of interest | Y | |
-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: Cytoplasmic dynein-1 bound to LIS1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20_4459: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90594 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7Z8G Accession code: 7Z8G / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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