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Yorodumi- EMDB-46849: structure of dynactin, dynein tail with TRAK2 from dynein-dynacti... -
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Basic information
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| Title | structure of dynactin, dynein tail with TRAK2 from dynein-dynactin-TRAK2 on microtubules | |||||||||
Map data | structure of dynactin, dynein tail with TRAK2 from dynein-dynactin-TRAK2 on microtubules | |||||||||
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Keywords | dynein / TRAK2 / dynactin / microtubule / MOTOR PROTEIN | |||||||||
| Function / homology | Function and homology informationRHOT1 GTPase cycle / RHOT2 GTPase cycle / dendritic transport of mitochondrion / mitochondrion distribution / : / Factors involved in megakaryocyte development and platelet production / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions ...RHOT1 GTPase cycle / RHOT2 GTPase cycle / dendritic transport of mitochondrion / mitochondrion distribution / : / Factors involved in megakaryocyte development and platelet production / retrograde axonal transport of mitochondrion / 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 / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / centriolar subdistal appendage / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / dynactin complex / positive regulation of neuromuscular junction development / centriole-centriole cohesion / 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 / F-actin capping protein complex / microtubule anchoring at centrosome / WASH complex / Recruitment of mitotic centrosome proteins and complexes / ventral spinal cord development / negative regulation of axonogenesis / retromer complex / cytoskeleton-dependent cytokinesis / microtubule plus-end / nuclear membrane disassembly / cellular response to cytochalasin B / positive regulation of microtubule nucleation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / melanosome transport / protein localization to adherens junction / barbed-end actin filament capping / GABA receptor binding / protein O-linked glycosylation / dense body / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / Neutrophil degranulation / non-motile cilium assembly / vesicle transport along microtubule / regulation of cell morphogenesis / dynein complex / retrograde transport, endosome to Golgi / adherens junction assembly / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / tight junction / microtubule associated complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / COPI-mediated anterograde transport / aorta development / ventricular septum development / microtubule-based movement / nuclear migration / neuromuscular process / apical junction complex / endosome to lysosome transport / dendrite morphogenesis / neuromuscular junction development / myosin binding / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / TPR domain binding / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / cell leading edge / motor behavior / dynein intermediate chain binding / dynein complex binding / microtubule organizing center / cleavage furrow / brush border / establishment of mitotic spindle orientation / kinesin binding / regulation of synaptic vesicle endocytosis / axonal growth cone Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
Authors | Rao Q / Chai P / Zhang K | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2024Title: Molecular basis for the assembly of the dynein transport machinery on microtubules. Authors: Qinhui Rao / Pengxin Chai / Kai Zhang / ![]() Abstract: Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has ...Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has been elusive. Here, we reveal detailed structural insights into microtubule-mediated DDA assembly using cryo-electron microscopy. We find that an adaptor-independent dynein-dynactin complex (DD) predominantly forms on microtubules in an intrinsic 2:1 stoichiometry, induced by spontaneous parallelization of dynein upon microtubule binding. Adaptors can squeeze in and exchange within the assembled microtubule-bound DD complex, which is enabled by relative rotations between dynein and dynactin, and further facilitated by dynein light intermediate chains that assist in an adaptor 'search' mechanism. Our findings elucidate the dynamic adaptability of the dynein transport machinery, and reveal a new mode for assembly of the motile complex. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_46849.map.gz | 13.5 MB | EMDB map data format | |
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| Header (meta data) | emd-46849-v30.xml emd-46849.xml | 38.5 KB 38.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_46849_fsc.xml | 6.3 KB | Display | FSC data file |
| Images | emd_46849.png | 55.7 KB | ||
| Filedesc metadata | emd-46849.cif.gz | 13.4 KB | ||
| Others | emd_46849_half_map_1.map.gz emd_46849_half_map_2.map.gz | 25 MB 25 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-46849 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-46849 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9dgvMC ![]() 9dgpC ![]() 9dgqC ![]() 9dgrC ![]() 9dgsC ![]() 9dgtC ![]() 9dguC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_46849.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | structure of dynactin, dynein tail with TRAK2 from dynein-dynactin-TRAK2 on microtubules | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 3.3 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: half map
| File | emd_46849_half_map_1.map | ||||||||||||
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| Annotation | half map | ||||||||||||
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| Density Histograms |
-Half map: half map
| File | emd_46849_half_map_2.map | ||||||||||||
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| Annotation | half map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Dynactin, dynein tail with TRAK2 of dynein-dynactin-TRAK2 complex...
+Supramolecule #1: Dynactin, dynein tail with TRAK2 of dynein-dynactin-TRAK2 complex...
+Macromolecule #1: Alpha-centractin
+Macromolecule #2: Actin, cytoplasmic 1
+Macromolecule #3: Actin-related protein 10
+Macromolecule #4: F-actin-capping protein subunit alpha-1
+Macromolecule #5: F-actin-capping protein subunit beta
+Macromolecule #6: Dynactin subunit 2
+Macromolecule #7: Dynactin subunit 3
+Macromolecule #8: Dynactin subunit 6
+Macromolecule #9: Dynactin subunit 5
+Macromolecule #10: Dynactin subunit 1
+Macromolecule #11: Dynactin subunit 4
+Macromolecule #12: Trafficking protein, kinesin binding 2
+Macromolecule #13: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #14: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #16: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #17: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.2 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS GLACIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
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About Yorodumi



Keywords
Authors
United States, 1 items
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Homo sapiens (human)

Processing
FIELD EMISSION GUN
