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Yorodumi- EMDB-11313: Cryo-EM structure of the dynactin complex at 3.8 Angstrom resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11313 | |||||||||
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Title | Cryo-EM structure of the dynactin complex at 3.8 Angstrom resolution | |||||||||
Map data | ||||||||||
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 / positive regulation of neuromuscular junction development / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / Gap junction degradation ...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 / positive regulation of neuromuscular junction development / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / 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 / centriole-centriole cohesion / ventral spinal cord development / microtubule anchoring at centrosome / WASH complex / F-actin capping protein complex / negative regulation of filopodium assembly / cellular response to cytochalasin B / melanosome transport / cytoskeleton-dependent cytokinesis / regulation of transepithelial transport / retromer complex / nuclear membrane disassembly / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / microtubule plus-end / positive regulation of microtubule nucleation / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / barbed-end actin filament capping / non-motile cilium assembly / adherens junction assembly / coronary vasculature development / 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 / retrograde transport, endosome to Golgi / tight junction / nuclear migration / regulation of norepinephrine uptake / COPI-mediated anterograde transport / aorta development / microtubule associated complex / motor behavior / NuA4 histone acetyltransferase complex / neuromuscular process / regulation of synaptic vesicle endocytosis / ventricular septum development / apical junction complex / establishment or maintenance of cell polarity / dynein complex binding / neuromuscular junction development / intercellular bridge / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / nitric-oxide synthase binding / cell leading edge / establishment of mitotic spindle orientation / cleavage furrow / brush border / kinesin binding / calyx of Held / regulation of protein localization to plasma membrane / microtubule-based process / stress fiber / cytoskeleton organization / regulation of mitotic spindle organization / axon cytoplasm / neuron projection maintenance / centriole / axonogenesis / sarcomere / mitotic spindle organization / ciliary basal body / actin filament / cell motility / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cell morphogenesis / cytoplasmic ribonucleoprotein granule / mitotic spindle Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_11313.map.gz | 287.7 MB | EMDB map data format | |
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Header (meta data) | emd-11313-v30.xml emd-11313.xml | 28 KB 28 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11313_fsc.xml | 15.2 KB | Display | FSC data file |
Images | emd_11313.png | 34.2 KB | ||
Masks | emd_11313_msk_1.map | 307.5 MB | Mask map | |
Others | emd_11313_half_map_1.map.gz emd_11313_half_map_2.map.gz | 244.9 MB 244.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11313 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11313 | HTTPS FTP |
-Related structure data
Related structure data | 6znlMC 6znmC 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_11313.map.gz / Format: CCP4 / Size: 307.5 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_11313_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11313_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11313_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Dynactin complex
+Supramolecule #1: Dynactin complex
+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 6
+Macromolecule #9: Dynactin subunit 5
+Macromolecule #10: Dynactin subunit 4
+Macromolecule #11: Dynactin subunit 1
+Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #13: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #14: 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: AB INITIO MODEL |
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Output model | PDB-6znl: |