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Open data
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Basic information
Entry | Database: PDB / ID: 8pr1 | ||||||||||||
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Title | Cytoplasmic dynein-B heavy chain bound to IC-LC tower | ||||||||||||
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![]() | MOTOR PROTEIN / Dynein / AAA-Atpase / LC8 / TCTEX1 | ||||||||||||
Function / homology | ![]() intracellular transport of viral protein in host cell / secretory vesicle / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / transport along microtubule / visual behavior / intraciliary retrograde transport / positive regulation of intracellular transport / dynein light chain binding / regulation of metaphase plate congression ...intracellular transport of viral protein in host cell / secretory vesicle / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / transport along microtubule / visual behavior / intraciliary retrograde transport / positive regulation of intracellular transport / dynein light chain binding / regulation of metaphase plate congression / motile cilium assembly / dynein heavy chain binding / establishment of spindle localization / Activation of BIM and translocation to mitochondria / axonemal dynein complex / positive regulation of spindle assembly / ciliary tip / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / dynein complex / regulation of G protein-coupled receptor signaling pathway / negative regulation of phosphorylation / P-body assembly / COPI-independent Golgi-to-ER retrograde traffic / microtubule-dependent intracellular transport of viral material towards nucleus / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / retrograde axonal transport / enzyme inhibitor activity / nuclear migration / centrosome localization / microtubule motor activity / dynein intermediate chain binding / Macroautophagy / microtubule-based movement / cytoplasmic microtubule / positive regulation of insulin secretion involved in cellular response to glucose stimulus / establishment of mitotic spindle orientation / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / Mitotic Prometaphase / cytoplasmic microtubule organization / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / axon cytoplasm / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / substantia nigra development / MHC class II antigen presentation / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / mitotic spindle / kinetochore / cilium / negative regulation of neurogenesis / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / host cell / late endosome / nervous system development / positive regulation of cold-induced thermogenesis / site of double-strand break / cell cortex / scaffold protein binding / secretory granule lumen / microtubule / vesicle / ficolin-1-rich granule lumen / cytoskeleton / symbiont entry into host cell / cell division / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 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 | ![]() | 652.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 76.4 KB | Display | |
Data in CIF | ![]() | 132.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17831MC ![]() 8pqvC ![]() 8pqwC ![]() 8pqyC ![]() 8pqzC ![]() 8pr0C ![]() 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
-Dynein light chain ... , 3 types, 6 molecules DEKLts
#1: Protein | Mass: 10381.899 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 12461.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Protein | Mass: 10934.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Cytoplasmic dynein 1 ... , 3 types, 6 molecules IJAGFH
#2: Protein | Mass: 68442.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 533055.125 Da / Num. of mol.: 2 / Mutation: R1567E, K1610E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 54173.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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: Cytoplasmic dynein-A heavy chain bound to dynactin p150 and IC-LC tower Type: COMPLEX / Entity ID: #1-#5 / 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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42405 / Symmetry type: POINT | ||||||||||||
Atomic model building | PDB-ID: 7Z8G Accession code: 7Z8G / Source name: PDB / Type: experimental model |