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Yorodumi- EMDB-14552: The barbed end complex of dynactin bound to BICDR1 and the cytopl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14552 | ||||||||||||
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Title | The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2, B1, B2) | ||||||||||||
Map data | The barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2). 1.2445 A/pix. | ||||||||||||
Sample |
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Keywords | Dynein / dynactin / cargo transport / activating adaptor / cytoskeleton / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / RHOF GTPase cycle / 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 ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / RHOF GTPase cycle / 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 / transport along microtubule / F-actin capping protein complex / WASH complex / dynein light chain binding / positive regulation of intracellular transport / negative regulation of filopodium assembly / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / positive regulation of spindle assembly / actin cortical patch / vesicle transport along microtubule / dynein complex / minus-end-directed microtubule motor activity / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / P-body assembly / regulation of cell morphogenesis / regulation of lamellipodium assembly / nuclear migration / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / centrosome localization / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / dynactin binding / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of mitotic spindle organization / axon cytoplasm / cytoskeleton organization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / mitotic spindle organization / cellular response to nerve growth factor stimulus / filopodium / RHO GTPases Activate Formins / cell morphogenesis / small GTPase binding / kinetochore / microtubule cytoskeleton organization / HCMV Early Events / Aggrephagy / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / neuron projection development / positive regulation of cold-induced thermogenesis / late endosome / actin binding / cell cortex / actin cytoskeleton organization / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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_14552.map.gz | 1.4 GB | EMDB map data format | |
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Header (meta data) | emd-14552-v30.xml emd-14552.xml | 36.4 KB 36.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14552_fsc.xml | 19.7 KB | Display | FSC data file |
Images | emd_14552.png | 105.2 KB | ||
Masks | emd_14552_msk_1.map | 1.7 GB | Mask map | |
Filedesc metadata | emd-14552.cif.gz | 11.8 KB | ||
Others | emd_14552_additional_1.map.gz emd_14552_half_map_1.map.gz emd_14552_half_map_2.map.gz | 1.4 GB 1.4 GB 1.4 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14552 | HTTPS FTP |
-Validation report
Summary document | emd_14552_validation.pdf.gz | 422.5 KB | Display | EMDB validaton report |
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Full document | emd_14552_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | emd_14552_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | emd_14552_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14552 | HTTPS FTP |
-Related structure data
Related structure data | 7z8iMC 7z8fC 7z8gC 7z8hC 7z8jC 7z8kC 7z8lC 7z8mC M: atomic model generated by this map C: citing same article (ref.) |
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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_14552.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2). 1.2445 A/pix. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2445 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14552_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: The barbed end complex of dynactin with BICDR-A...
File | emd_14552_additional_1.map | ||||||||||||
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Annotation | The barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2). Unsharpenned map fit to the consensus map rescaled to 1.2445 A/pix. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of the barbed end complex...
File | emd_14552_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of the barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2) after fitting to the consensus map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the barbed end complex...
File | emd_14552_half_map_2.map | ||||||||||||
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Annotation | Half map 2 of the barbed end complex of dynactin with BICDR-A and dynein tails (A2, B1, B2) after fitting to the consensus map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #3: F-actin capping protein beta subunit
+Macromolecule #4: BICD family-like cargo adapter 1
+Macromolecule #5: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #6: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #7: Cytoplasmic dynein 1 light intermediate chain 2
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
-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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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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7z8i: |