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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 / : / 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 ...Golgi to secretory granule transport / : / 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 / centriole-centriole cohesion / visual behavior / positive regulation of neuromuscular junction development / 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 / nuclear membrane disassembly / 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 / Intraflagellar transport / 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 / establishment of spindle localization / protein localization to adherens junction / barbed-end actin filament capping / dense body / Neutrophil degranulation / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / non-motile cilium assembly / regulation of cell morphogenesis / vesicle transport along microtubule / retrograde transport, endosome to Golgi / adherens junction assembly / retrograde axonal transport / COPI-independent Golgi-to-ER retrograde traffic / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / 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 / P-body assembly / centrosome localization / 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 / dynein intermediate chain binding / NuA4 histone acetyltransferase complex / motor behavior / cell leading edge / cortical cytoskeleton 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 | http://ftp.pdbj.org/pub/emdb/structures/EMD-14549 ftp://ftp.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
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Z (Sec.)
Y (Row.)
X (Col.)
























FIELD EMISSION GUN
