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Yorodumi- EMDB-73178: Dynactin and dynein-1 tail region of dynein-dynactin complex on m... -
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Basic information
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| Title | Dynactin and dynein-1 tail region of dynein-dynactin complex on microtubule in the presence of LIS1 | |||||||||
Map data | Sharpened map of dynactin and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1 | |||||||||
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Keywords | Dynein-1 / Dynactin / MOTOR PROTEIN | |||||||||
| Function / homology | Function and homology information: / 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 ...: / 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 / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / dynactin complex / centriolar subdistal appendage / 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 / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / nuclear membrane disassembly / F-actin capping protein complex / WASH complex / dynein light chain binding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / cytoskeleton-dependent cytokinesis / retromer complex / dynein complex / microtubule plus-end / cellular response to cytochalasin B / positive regulation of microtubule nucleation / positive regulation of intracellular transport / regulation of transepithelial transport / regulation of metaphase plate congression / positive regulation of spindle assembly / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / melanosome transport / protein localization to adherens junction / establishment of spindle localization / barbed-end actin filament capping / dense body / Tat protein binding / Neutrophil degranulation / coronary vasculature development / postsynaptic actin cytoskeleton / non-motile cilium assembly / regulation of cell morphogenesis / adherens junction assembly / retrograde transport, endosome to Golgi / retrograde axonal transport / apical protein localization / COPI-independent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / minus-end-directed microtubule motor activity / MHC class II antigen presentation / microtubule associated complex / Recruitment of NuMA to mitotic centrosomes / dynein light intermediate chain binding / cytoplasmic dynein complex / tight junction / microtubule motor activity / COPI-mediated anterograde transport / ventricular septum development / aorta development / microtubule-based movement / nuclear migration / apical junction complex / neuromuscular process / establishment of mitotic spindle orientation / neuromuscular junction development / regulation of norepinephrine uptake / transporter regulator activity / NuA4 histone acetyltransferase complex / dynein intermediate chain binding / motor behavior / establishment or maintenance of cell polarity / cell leading edge / cortical cytoskeleton / cleavage furrow / microtubule organizing center / dynein complex binding / nitric-oxide synthase binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.07 Å | |||||||||
Authors | Yang J / Rao Q / Chai P / Zhang K | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2026Title: Roles of microtubules and LIS1 in dynein transport machinery assembly. Authors: Qinhui Rao / Jun Yang / Pengxin Chai / Steven Markus / Kai Zhang / ![]() Abstract: Cytoplasmic dynein-1, a microtubule (MT)-based motor protein, requires dynactin and a coiled-coil adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The roles of MTs and dynein ...Cytoplasmic dynein-1, a microtubule (MT)-based motor protein, requires dynactin and a coiled-coil adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The roles of MTs and dynein regulator lissencephaly-1 (LIS1) in DDA assembly have remained elusive. Here we use cryo-electron microscopy to determine the structural basis of MT- and LIS1-mediated DDA assembly. We show that an adaptor-independent dynein-dynactin complex spontaneously forms on MTs with an intrinsic 2:1 stoichiometry in a highly efficient manner, driven by parallel alignment of dynein tails upon MT binding. Adaptors can wedge into and exchange within the assembled MT-bound dynein-dynactin complex; these processes are enabled by relative rotations between dynein and dynactin and facilitated by the dynein light-intermediate chains that assist the adaptor 'search' mechanism. Although LIS1 is dispensable for efficient DD(A)-MT assembly, its presence expands the conformational landscape of DD(A) assemblies on MTs. Cryo-electron microscopy reveals that LIS1 bridges dynactin p150 and dynein in both the closed Phi-like and open prepowerstroke states, stabilizing low-MT-affinity intermediates that tether dynein molecules in proximity to MTs and prime them for subsequent DD(A) assembly through alternative pathways. These findings demonstrate the dynamic adaptability of the dynein transport machinery and the coordinated roles of MTs and LIS1 in DDA assembly. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_73178.map.gz | 450.2 MB | EMDB map data format | |
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| Header (meta data) | emd-73178-v30.xml emd-73178.xml | 44.3 KB 44.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_73178_fsc.xml | 16.5 KB | Display | FSC data file |
| Images | emd_73178.png | 57.5 KB | ||
| Masks | emd_73178_msk_1.map | 476.8 MB | Mask map | |
| Filedesc metadata | emd-73178.cif.gz | 13.3 KB | ||
| Others | emd_73178_additional_1.map.gz emd_73178_half_map_1.map.gz emd_73178_half_map_2.map.gz | 238.1 MB 443 MB 443 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-73178 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-73178 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9yngMC ![]() 9dgpC ![]() 9dgqC ![]() 9dgrC ![]() 9dgsC ![]() 9dgtC ![]() 9dguC ![]() 9dgvC ![]() 9yncC ![]() 9yndC ![]() 9yneC ![]() 9ynfC ![]() 9ynhC 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_73178.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Sharpened map of dynactin and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1 | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_73178_msk_1.map | ||||||||||||
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| Density Histograms |
-Additional map: Unsharpened map of dynactin and dynein tail region...
| File | emd_73178_additional_1.map | ||||||||||||
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| Annotation | Unsharpened map of dynactin and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1 | ||||||||||||
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| Density Histograms |
-Half map: Half map of dynactin and dynein tail region...
| File | emd_73178_half_map_1.map | ||||||||||||
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| Annotation | Half map of dynactin and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half map of dynactin and dynein tail region...
| File | emd_73178_half_map_2.map | ||||||||||||
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| Annotation | Half map of dynactin and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1 | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Dynactin and dynein tail region of dynein-dynactin complex on mic...
+Supramolecule #1: Dynactin and dynein tail region of dynein-dynactin complex on mic...
+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: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #13: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #14: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #15: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #16: 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
| Concentration | 2 mg/mL |
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| Buffer | pH: 7.2 |
| 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 | C2 aperture diameter: 30.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN
