+Open data
-Basic information
Entry | Database: PDB / ID: 8pr1 | ||||||||||||
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Title | Cytoplasmic dynein-B heavy chain bound to IC-LC tower | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Dynein / AAA-Atpase / LC8 / TCTEX1 | ||||||||||||
Function / homology | Function and homology information intracellular transport of viral protein in host cell / secretory vesicle / positive regulation of non-motile cilium assembly / transport along microtubule / intraciliary retrograde transport / visual behavior / dynein light chain binding / mitocytosis / dynein heavy chain binding / positive regulation of intracellular transport ...intracellular transport of viral protein in host cell / secretory vesicle / positive regulation of non-motile cilium assembly / transport along microtubule / intraciliary retrograde transport / visual behavior / dynein light chain binding / mitocytosis / dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / motile cilium assembly / establishment of spindle localization / Activation of BIM and translocation to mitochondria / 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 / retrograde axonal transport / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / enzyme inhibitor activity / nuclear migration / centrosome localization / microtubule motor activity / dynein intermediate chain binding / Macroautophagy / microtubule-based movement / cytoplasmic microtubule / host cell / spermatid development / establishment of mitotic spindle orientation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / substantia nigra development / MHC class II antigen presentation / nitric-oxide synthase regulator activity / AURKA Activation by TPX2 / mitotic spindle organization / cellular response to nerve growth factor stimulus / regulation of mitochondrial membrane potential / filopodium / RHO GTPases Activate Formins / cilium / spindle / kinetochore / mitotic spindle / microtubule cytoskeleton organization / Aggrephagy / negative regulation of neurogenesis / HCMV Early Events / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / late endosome / nervous system development / positive regulation of cold-induced thermogenesis / cell cortex / scaffold protein binding / secretory granule lumen / microtubule / vesicle / ficolin-1-rich granule lumen / cytoskeleton / symbiont entry into host cell / protein domain specific binding / cell division / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 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 | 8pr1.cif.gz | 652.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pr1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8pr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8pr1 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8pr1 | HTTPS FTP |
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-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 (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
-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.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63167 #3: Protein | Mass: 12461.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLT1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63172 #6: Protein | Mass: 10934.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97 |
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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.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409 #4: Protein | Mass: 533055.125 Da / Num. of mol.: 2 / 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 #5: Protein | Mass: 54173.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237 |
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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-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: 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 |
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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 |