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Open data
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Basic information
Entry | Database: PDB / ID: 8ptk | ||||||||||||
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Title | Composite structure of Dynein-Dynactin-JIP3-LIS1 | ||||||||||||
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![]() | MOTOR PROTEIN / Dynein / AAA-Atpase / p150 / LIS1 / Dynactin / JIP3 | ||||||||||||
Function / homology | ![]() RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / intracellular transport of viral protein in host cell ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / intracellular transport of viral protein in host cell / retrograde axonal transport of mitochondrion / UCH proteinases / corpus callosum morphogenesis / secretory vesicle / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / centriolar subdistal appendage / positive regulation of neuromuscular junction development / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / dynactin complex / 1-alkyl-2-acetylglycerophosphocholine esterase complex / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / centriole-centriole cohesion / Recruitment of mitotic centrosome proteins and complexes / maintenance of centrosome location / negative regulation of phosphorylation / microtubule anchoring at centrosome / F-actin capping protein complex / platelet activating factor metabolic process / WASH complex / transport along microtubule / intraciliary retrograde transport / visual behavior / radial glia-guided pyramidal neuron migration / acrosome assembly / central region of growth cone / cerebral cortex neuron differentiation / ventral spinal cord development / dynein light chain binding / establishment of centrosome localization / microtubule sliding / positive regulation of embryonic development / dynein heavy chain binding / anterograde axonal protein transport / positive regulation of cytokine-mediated signaling pathway / motile cilium assembly / Activation of BIM and translocation to mitochondria / microtubule organizing center organization / interneuron migration / retromer complex / cytoskeleton-dependent cytokinesis / layer formation in cerebral cortex / cellular response to cytochalasin B / ciliary tip / microtubule plus-end / auditory receptor cell development / nuclear membrane disassembly / astral microtubule / regulation of transepithelial transport / Intraflagellar transport / MAP-kinase scaffold activity / positive regulation of microtubule nucleation / morphogenesis of a polarized epithelium / positive regulation of dendritic spine morphogenesis / structural constituent of postsynaptic actin cytoskeleton / cortical microtubule organization / positive regulation of intracellular transport / negative regulation of nitric oxide biosynthetic process / protein localization to adherens junction / myeloid leukocyte migration / reelin-mediated signaling pathway / melanosome transport / dense body / regulation of metaphase plate congression / postsynaptic actin cytoskeleton / barbed-end actin filament capping / establishment of spindle localization / Neutrophil degranulation / Tat protein binding / positive regulation of spindle assembly / JUN kinase binding / regulation of G protein-coupled receptor signaling pathway / stereocilium / osteoclast development / coronary vasculature development / non-motile cilium assembly / microtubule plus-end binding / brain morphogenesis Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 548.4 KB | Display | |
Data in CIF | ![]() | 987.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17873MC ![]() 8pqvC ![]() 8pqwC ![]() 8pqyC ![]() 8pqzC ![]() 8pr0C ![]() 8pr1C ![]() 8pr2C ![]() 8pr3C ![]() 8pr4C ![]() 8pr5C 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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1 |
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Components
-Protein , 8 types, 19 molecules 1234ABCDEFGIHJKLUXx
#1: Protein | Mass: 46709.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | | Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | | Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 65975.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Dynactin subunit ... , 5 types, 10 molecules MNPQORSTWY
#7: Protein | Mass: 44704.414 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 21192.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 142015.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | | Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | | Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Dynein light chain ... , 3 types, 12 molecules abdiklvystwz
#14: Protein | Mass: 10381.899 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #18: Protein | Mass: 12461.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #19: Protein | Mass: 10934.576 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Cytoplasmic dynein 1 ... , 3 types, 12 molecules efmnghopjqru
#15: Protein | Mass: 533055.125 Da / Num. of mol.: 4 / Mutation: R1567E, K1610E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #16: Protein | Mass: 68442.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #17: Protein | Mass: 54173.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 35 molecules 








#20: Chemical | ChemComp-ADP / #21: Chemical | ChemComp-ATP / #22: Chemical | #23: Chemical | ChemComp-MG / #24: Chemical | ChemComp-ANP / |
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-Details
Has ligand of interest | Y |
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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
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Source (natural) |
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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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 10 Å / Resolution method: OTHER / Num. of particles: 700290 / Symmetry type: POINT | ||||||||||||
Atomic model building | PDB-ID: 7Z8G Accession code: 7Z8G / Source name: PDB / Type: experimental model |