+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14559 | ||||||||||||
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Title | The pointed end complex of dynactin bound to BICDR1 | ||||||||||||
Map data | The pointed end complex of dynactin, Arp1/actin filament subunits, and BICDR1 Spindly motif. 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 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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs ...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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Clathrin-mediated endocytosis / RHOF GTPase cycle / dynactin complex / 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 / vesicle transport along microtubule / structural constituent of postsynaptic actin cytoskeleton / dense body / dynein complex / Neutrophil degranulation / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / dynein complex binding / NuA4 histone acetyltransferase complex / dynactin binding / microtubule-based process / stress fiber / axon cytoplasm / sarcomere / mitotic spindle organization / axonogenesis / actin filament / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinetochore / small GTPase binding / neuron projection development / actin cytoskeleton / cell cortex / cytoskeleton / hydrolase activity / axon / focal adhesion / centrosome / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 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_14559.map.gz | 948.3 MB | EMDB map data format | |
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Header (meta data) | emd-14559-v30.xml emd-14559.xml | 31 KB 31 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14559_fsc.xml | 19.7 KB | Display | FSC data file |
Images | emd_14559.png | 71.5 KB | ||
Masks | emd_14559_msk_1.map | 1.7 GB | Mask map | |
Filedesc metadata | emd-14559.cif.gz | 8.8 KB | ||
Others | emd_14559_half_map_1.map.gz emd_14559_half_map_2.map.gz | 947.9 MB 947.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14559 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14559 | HTTPS FTP |
-Validation report
Summary document | emd_14559_validation.pdf.gz | 530.2 KB | Display | EMDB validaton report |
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Full document | emd_14559_full_validation.pdf.gz | 529.8 KB | Display | |
Data in XML | emd_14559_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | emd_14559_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14559 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14559 | HTTPS FTP |
-Related structure data
Related structure data | 7z8mMC 7z8fC 7z8gC 7z8hC 7z8iC 7z8jC 7z8kC 7z8lC 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_14559.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The pointed end complex of dynactin, Arp1/actin filament subunits, and BICDR1 Spindly motif. 1.2445 A/pix. | ||||||||||||||||||||
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_14559_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of the pointed end after fitting to the consensus map.
File | emd_14559_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of the pointed end after fitting to the consensus map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the pointed end after fitting to the consensus map.
File | emd_14559_half_map_2.map | ||||||||||||
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Annotation | Half map 2 of the pointed end 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: Dynactin subunit 2
+Macromolecule #2: BICD family-like cargo adapter 1
+Macromolecule #3: Dynactin 6
+Macromolecule #4: Dynactin subunit 4
+Macromolecule #5: Arp11
+Macromolecule #6: ARP1 actin related protein 1 homolog A
+Macromolecule #7: Actin, cytoplasmic 1
+Macromolecule #8: Dynactin subunit 5
+Macromolecule #9: ZINC ION
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE
-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-7z8m: |