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Yorodumi- PDB-8pqw: Cytoplasmic dynein-1 motor domain bound to dynactin-p150glued and LIS1 -
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-Basic information
Entry | Database: PDB / ID: 8pqw | ||||||||||||
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Title | Cytoplasmic dynein-1 motor domain bound to dynactin-p150glued and LIS1 | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Dynein / AAA-Atpase / p150 / LIS1 | ||||||||||||
Function / homology | Function and homology information Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration ...Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / 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 / positive regulation of neuromuscular junction development / centriolar subdistal appendage / maintenance of centrosome location / microtubule sliding / centriole-centriole cohesion / transport along microtubule / platelet activating factor metabolic process / dynein light chain binding / ventral spinal cord development / microtubule anchoring at centrosome / acrosome assembly / radial glia-guided pyramidal neuron migration / microtubule organizing center organization / cerebral cortex neuron differentiation / dynein heavy chain binding / positive regulation of intracellular transport / central region of growth cone / 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 / melanosome transport / astral microtubule / positive regulation of spindle assembly / layer formation in cerebral cortex / nuclear membrane disassembly / retromer complex / auditory receptor cell development / microtubule plus-end / positive regulation of dendritic spine morphogenesis / vesicle transport along microtubule / positive regulation of microtubule nucleation / stem cell division / stereocilium / myeloid leukocyte migration / dynein complex / P-body assembly / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / negative regulation of JNK cascade / retrograde axonal transport / minus-end-directed microtubule motor activity / non-motile cilium assembly / cytoplasmic dynein complex / dynein light intermediate chain binding / brain morphogenesis / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / motile cilium / MHC class II antigen presentation / retrograde transport, endosome to Golgi / nuclear migration / osteoclast development / COPI-mediated anterograde transport / microtubule associated complex / motor behavior / neuromuscular process / kinesin complex / microtubule motor activity / dynein intermediate chain binding / neuromuscular junction development / dynein complex binding / cochlea development / intercellular bridge / microtubule-based movement / transmission of nerve impulse / cytoplasmic microtubule / cell leading edge / germ cell development / establishment of mitotic spindle orientation / 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 / microtubule-based process / COPI-mediated anterograde transport / lipid catabolic process / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Singh, K. / Lau, C.K. / Manigrasso, G. / Gassmann, R. / Carter, A.P. | ||||||||||||
Funding support | United Kingdom, European Union, 3items
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Citation | Journal: Science / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pqw.cif.gz | 801.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pqw.ent.gz | 578.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/8pqw ftp://data.pdbj.org/pub/pdb/validation_reports/pq/8pqw | HTTPS FTP |
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-Related structure data
Related structure data | 17826MC 8pqvC 8pqyC 8pqzC 8pr0C 8pr1C 8pr2C 8pr3C 8pr4C 8pr5C 8ptkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytoplasmic dynein 1 ... , 2 types, 3 molecules AHI
#1: Protein | Mass: 533055.125 Da / Num. of mol.: 1 / Mutation: R1567E, K1610E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204 |
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#4: Protein | Mass: 68442.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409 |
-Protein , 2 types, 6 molecules BCDEFG
#2: Protein | Mass: 46709.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43034 #3: Protein | Mass: 142015.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B8J2 |
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-Non-polymers , 3 types, 6 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ATP / | |
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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 |
-Sample preparation
Component | Name: Cytoplasmic dynein-1 bound to dynactin p150 and LIS1 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-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: 4.2 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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