+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11317 | |||||||||
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Title | The pointed end complex of dynactin bound to BICDR1 | |||||||||
Map data | ||||||||||
Sample |
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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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...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 / cellular response to cytochalasin B / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / vesicle transport along microtubule / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / adherens junction assembly / coronary vasculature development / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / 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 / regulation of norepinephrine uptake / aorta development / COPI-mediated anterograde transport / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / ventricular septum development / establishment or maintenance of cell polarity / dynein complex binding / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / nitric-oxide synthase binding / dynactin binding / brush border / kinesin binding / calyx of Held / regulation of protein localization to plasma membrane / microtubule-based process / stress fiber / axon cytoplasm / sarcomere / axonogenesis / mitotic spindle organization / cell motility / actin filament / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / kinetochore / small GTPase binding / cytoplasmic ribonucleoprotein granule / neuron projection development / nucleosome / actin cytoskeleton / lamellipodium / cell cortex / nuclear membrane / microtubule / cytoskeleton / hydrolase activity / regulation of cell cycle / ribonucleoprotein complex / axon / focal adhesion / centrosome / glutamatergic synapse / synapse / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / nucleus / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Mus musculus (house mouse) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Lau CK / Lacey SE / Carter AP | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Authors: Clinton K Lau / Francis J O'Reilly / Balaji Santhanam / Samuel E Lacey / Juri Rappsilber / Andrew P Carter / Abstract: Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled- ...Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high-resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin's filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11317.map.gz | 62.3 MB | EMDB map data format | |
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Header (meta data) | emd-11317-v30.xml emd-11317.xml | 29.6 KB 29.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11317_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_11317.png | 40.9 KB | ||
Masks | emd_11317_msk_1.map | 67 MB | Mask map | |
Others | emd_11317_additional.map.gz emd_11317_half_map_1.map.gz emd_11317_half_map_2.map.gz | 61.7 MB 51.7 MB 51.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11317 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11317 | HTTPS FTP |
-Related structure data
Related structure data | 6znmMC 6znlC 6znnC 6znoC 6zo4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11317.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11317_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Main map filtered to 6 Angstrom and not sharpened
File | emd_11317_additional.map | ||||||||||||
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Annotation | Main map filtered to 6 Angstrom and not sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11317_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11317_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Dynein-Dynactin-BICDR1 complex
+Supramolecule #1: Dynein-Dynactin-BICDR1 complex
+Supramolecule #2: Dynactin
+Supramolecule #3: BICDR1
+Macromolecule #1: ARP1 actin related protein 1 homolog A
+Macromolecule #2: Actin, cytoplasmic 1
+Macromolecule #3: Arp11
+Macromolecule #4: Dynactin subunit 2
+Macromolecule #5: Dynactin 6
+Macromolecule #6: Dynactin subunit 5
+Macromolecule #7: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1...
+Macromolecule #8: Dynactin subunit 4
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6znm: |