+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17873 | ||||||||||||
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Title | Composite structure of Dynein-Dynactin-JIP3-LIS1 | ||||||||||||
Map data | Composite map of Dynein-Dynactin-JIP3-LIS1 filtered to 10 angstrom resolution | ||||||||||||
Sample |
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Keywords | Dynein / AAA-Atpase / p150 / LIS1 / MOTOR PROTEIN / Dynactin / JIP3 | ||||||||||||
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 / intracellular transport of viral protein in host cell / corpus callosum morphogenesis / secretory vesicle / establishment of planar polarity of embryonic epithelium ...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 / intracellular transport of viral protein in host cell / corpus callosum morphogenesis / secretory vesicle / 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 / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / maintenance of centrosome location / microtubule sliding / dynactin complex / positive regulation of non-motile cilium assembly / Clathrin-mediated endocytosis / centriole-centriole cohesion / transport along microtubule / intraciliary retrograde transport / visual behavior / platelet activating factor metabolic process / dynein light chain binding / ventral spinal cord development / microtubule anchoring at centrosome / WASH complex / acrosome assembly / radial glia-guided pyramidal neuron migration / microtubule organizing center organization / F-actin capping protein complex / cerebral cortex neuron differentiation / mitocytosis / motile cilium assembly / dynein heavy chain binding / negative regulation of filopodium assembly / central region of growth cone / positive regulation of intracellular transport / positive regulation of embryonic development / reelin-mediated signaling pathway / regulation of metaphase plate congression / establishment of centrosome localization / anterograde axonal protein transport / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / cellular response to cytochalasin B / establishment of spindle localization / Activation of BIM and translocation to mitochondria / melanosome transport / astral microtubule / cytoskeleton-dependent cytokinesis / ciliary tip / positive regulation of spindle assembly / layer formation in cerebral cortex / regulation of transepithelial transport / retromer complex / nuclear membrane disassembly / structural constituent of postsynaptic actin cytoskeleton / auditory receptor cell development / morphogenesis of a polarized epithelium / microtubule plus-end / positive regulation of dendritic spine morphogenesis / vesicle transport along microtubule / positive regulation of microtubule nucleation / Intraflagellar transport / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / stem cell division / negative regulation of nitric oxide biosynthetic process / Neutrophil degranulation / MAP-kinase scaffold activity / stereocilium / negative regulation of phosphorylation / P-body assembly / myeloid leukocyte migration / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / regulation of G protein-coupled receptor signaling pathway / apical protein localization / microtubule plus-end binding / microtubule-dependent intracellular transport of viral material towards nucleus / minus-end-directed microtubule motor activity / barbed-end actin filament capping / cytoplasmic dynein complex / JUN kinase binding / negative regulation of JNK cascade Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | ||||||||||||
Authors | Singh K / Lau CK / Manigrasso G / Gassmann R / Carter AP | ||||||||||||
Funding support | United Kingdom, European Union, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17873.map.gz | 917.7 MB | EMDB map data format | |
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Header (meta data) | emd-17873-v30.xml emd-17873.xml | 45.2 KB 45.2 KB | Display Display | EMDB header |
Images | emd_17873.png | 45.7 KB | ||
Filedesc metadata | emd-17873.cif.gz | 14.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17873 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17873 | HTTPS FTP |
-Related structure data
Related structure data | 8ptkMC 8pqvC 8pqwC 8pqyC 8pqzC 8pr0C 8pr1C 8pr2C 8pr3C 8pr4C 8pr5C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17873.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map of Dynein-Dynactin-JIP3-LIS1 filtered to 10 angstrom resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Composite structure of Dynein-Dynactin-JIP3-LIS1
+Supramolecule #1: Composite structure of Dynein-Dynactin-JIP3-LIS1
+Supramolecule #2: Dynactin subunits
+Supramolecule #3: Dynein and JIP3
+Macromolecule #1: Platelet-activating factor acetylhydrolase IB subunit beta
+Macromolecule #2: ARP1 actin related protein 1 homolog A
+Macromolecule #3: Actin, cytoplasmic 1
+Macromolecule #4: Arp11
+Macromolecule #5: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #6: F-actin-capping protein subunit beta
+Macromolecule #7: Dynactin subunit 2
+Macromolecule #8: Dynactin subunit 3
+Macromolecule #9: Dynactin subunit 1
+Macromolecule #10: Dynactin 6
+Macromolecule #11: Dynactin subunit 5
+Macromolecule #12: C-Jun-amino-terminal kinase-interacting protein 3
+Macromolecule #13: Dynactin subunit 4
+Macromolecule #14: Dynein light chain 1, cytoplasmic
+Macromolecule #15: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #16: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #17: Cytoplasmic dynein 1 light intermediate chain 2
+Macromolecule #18: Dynein light chain Tctex-type 1
+Macromolecule #19: Dynein light chain roadblock-type 1
+Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #21: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #22: ZINC ION
+Macromolecule #23: MAGNESIUM ION
+Macromolecule #24: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Number images used: 700290 |