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Open data
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Basic information
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| Title | Composite structure of dynein-dynactin-BICDR on microtubules | ||||||||||||
Map data | Composite structure of the dynein-dynactin-BICDR1 complex | ||||||||||||
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Keywords | Dynein / dynactin / cargo transport / activating adaptor / cytoskeleton / STRUCTURAL PROTEIN | ||||||||||||
| Function / homology | Function and homology informationGolgi to secretory granule transport / Advanced glycosylation endproduct receptor signaling / sterol sensor activity / 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 ...Golgi to secretory granule transport / Advanced glycosylation endproduct receptor signaling / sterol sensor activity / 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 / RHOF GTPase cycle / 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 / GBP-mediated host defense / Platelet degranulation / visual behavior / Gap junction degradation / Formation of annular gap junctions / UCH proteinases / centriolar subdistal appendage / ventral spinal cord development / Clathrin-mediated endocytosis / centriole-centriole cohesion / dynein-driven meiotic oscillatory nuclear movement / positive regulation of neuromuscular junction development / dynactin complex / 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 / F-actin capping protein complex / WASH complex / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / outer dynein arm / Activation of STAT3 by cadherin engagement / dynein light chain binding / lysosome to ER cholesterol transport / transport along microtubule / dynein heavy chain binding / retromer complex / cytoskeleton-dependent cytokinesis / dynein complex / mitotic nuclear membrane disassembly / positive regulation of microtubule nucleation / Intraflagellar transport / cellular response to cytochalasin B / intraciliary retrograde transport / positive regulation of intracellular transport / positive regulation of spindle assembly / regulation of transepithelial transport / regulation of metaphase plate congression / microtubule plus-end / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / barbed-end actin filament capping / non-motile cilium assembly / establishment of spindle localization / Neutrophil degranulation / dense body / Tat protein binding / motor behavior / vesicle transport along microtubule / positive regulation of mitotic cell cycle spindle assembly checkpoint / postsynaptic actin cytoskeleton / apical protein localization / retrograde axonal transport / neuron cellular homeostasis / retrograde transport, endosome to Golgi / adherens junction assembly / COPI-independent Golgi-to-ER retrograde traffic / microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / minus-end-directed microtubule motor activity / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule associated complex / dynein light intermediate chain binding / MHC class II antigen presentation / cytoplasmic dynein complex / Recruitment of NuMA to mitotic centrosomes / nuclear migration / tight junction / neuromuscular process / microtubule-based movement / COPI-mediated anterograde transport / apical junction complex / intercellular bridge / male germ cell nucleus / NuA4 histone acetyltransferase complex / dynein intermediate chain binding / cell leading edge Similarity search - Function | ||||||||||||
| Biological species | Homo sapiens (human) / ![]() ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | ||||||||||||
Authors | Chaaban S / Carter AP | ||||||||||||
| Funding support | United Kingdom, European Union, 3 items
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Citation | Journal: Nature / Year: 2022Title: Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Authors: Sami Chaaban / Andrew P Carter / ![]() Abstract: Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between ...Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour. Different coiled-coil adaptors are linked to different cargos, and some share motifs known to contact sites on dynein and dynactin. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos. | ||||||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_14549.map.gz | 201.4 MB | EMDB map data format | |
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| Header (meta data) | emd-14549-v30.xml emd-14549.xml | 44.7 KB 44.7 KB | Display Display | EMDB header |
| Images | emd_14549.png | 61.2 KB | ||
| Filedesc metadata | emd-14549.cif.gz | 14.5 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-14549 ftp://data.pdbj.org/pub/emdb/structures/EMD-14549 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7z8fMC ![]() 7z8gC ![]() 7z8hC ![]() 7z8iC ![]() 7z8jC ![]() 7z8kC ![]() 7z8lC ![]() 7z8mC C: citing same article ( M: atomic model generated by this map |
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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_14549.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Composite structure of the dynein-dynactin-BICDR1 complex | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 2.489 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Complex of dynein, dynactin, and BICDR1 bound to microtubules
+Supramolecule #1: Complex of dynein, dynactin, and BICDR1 bound to microtubules
+Supramolecule #2: Dynein, cytoplasmic 1
+Supramolecule #3: Dynactin
+Supramolecule #4: BICDR1
+Macromolecule #1: ARP1 actin related protein 1 homolog A
+Macromolecule #2: Actin, cytoplasmic 1
+Macromolecule #3: Arp11
+Macromolecule #4: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #5: F-actin capping protein beta subunit
+Macromolecule #6: Dynactin subunit 2
+Macromolecule #7: Dynactin subunit 3
+Macromolecule #8: Dynactin subunit 1
+Macromolecule #9: Dynactin 6
+Macromolecule #10: Dynactin subunit 5
+Macromolecule #11: BICD family-like cargo adapter 1
+Macromolecule #12: Dynactin subunit 4
+Macromolecule #13: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #14: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #15: Cytoplasmic dynein 1 light intermediate chain 2
+Macromolecule #16: Dynein light chain roadblock-type 1
+Macromolecule #17: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #18: MAGNESIUM ION
+Macromolecule #19: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #20: ZINC ION
+Macromolecule #21: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-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 Component:
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: 20 second incubation. |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 14 / Number real images: 88715 / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2 Details: Images were collected in movie-mode and fractionated into 53 movie frames |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
| Startup model | Type of model: OTHER |
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| Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: RELION Details: This is a composite of multiple maps with resolutions ranging from 3.3-12.2 A, resampled on a grid of 2.5 A/pix Number images used: 628033 |
| Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
| Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
-Atomic model buiding 1
| Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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| Output model | ![]() PDB-7z8f: |
Movie
Controller
About Yorodumi




Keywords
Homo sapiens (human)
Authors
United Kingdom, European Union, 3 items
Citation








































Z (Sec.)
Y (Row.)
X (Col.)
























FIELD EMISSION GUN
