+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14549 | ||||||||||||
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Title | Composite structure of dynein-dynactin-BICDR on microtubules | ||||||||||||
Map data | Composite structure of the dynein-dynactin-BICDR1 complex | ||||||||||||
Sample |
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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 / Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions ...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 / Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / 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 / dynactin complex / Clathrin-mediated endocytosis / transport along microtubule / visual behavior / dynein light chain binding / WASH complex / F-actin capping protein complex / dynein heavy chain binding / negative regulation of filopodium assembly / positive regulation of intracellular transport / regulation of metaphase plate congression / cellular response to cytochalasin B / establishment of spindle localization / cytoskeleton-dependent cytokinesis / ciliary tip / positive regulation of spindle assembly / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / vesicle transport along microtubule / Intraflagellar transport / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / P-body assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / apical protein localization / minus-end-directed microtubule motor activity / barbed-end actin filament capping / cytoplasmic dynein complex / retrograde axonal transport / adherens junction assembly / coronary vasculature development / dynein light intermediate chain binding / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / regulation of cell morphogenesis / RHO GTPases Activate Formins / regulation of lamellipodium assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / tight junction / nuclear migration / regulation of norepinephrine uptake / COPI-mediated anterograde transport / aorta development / NuA4 histone acetyltransferase complex / centrosome localization / regulation of synaptic vesicle endocytosis / ventricular septum development / microtubule motor activity / apical junction complex / establishment or maintenance of cell polarity / dynein intermediate chain binding / dynein complex binding / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / microtubule-based movement / nitric-oxide synthase binding / dynactin binding / cleavage furrow / brush border / kinesin binding / calyx of Held / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of protein localization to plasma membrane / microtubule-based process / COPI-mediated anterograde transport / stress granule assembly / cytoplasmic microtubule organization / stress fiber / Mitotic Prometaphase / cytoskeleton organization / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) / pig (pig) | ||||||||||||
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: 2022 Title: 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
Supplemental images |
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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 | 43.9 KB 43.9 KB | Display Display | EMDB header |
Images | emd_14549.png | 61.2 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 (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_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
-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 |
-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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
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 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7z8f: |