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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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Keywords | Dynactin / Complex / Scaffold / Cytoskeleton / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 / WASH complex / F-actin capping protein complex / negative regulation of filopodium assembly / cytoskeleton-dependent cytokinesis / cell tip / structural constituent of postsynaptic actin cytoskeleton / microtubule plus-end / dense body / dynein complex / Neutrophil degranulation / barbed-end actin filament capping / microtubule plus-end binding / regulation of cell morphogenesis / regulation of lamellipodium assembly / nuclear migration / 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 / microtubule associated complex / COPI-mediated anterograde transport / dynein complex binding / NuA4 histone acetyltransferase complex / establishment of mitotic spindle orientation / cleavage furrow / stress fiber / cytoplasmic microtubule organization / axon cytoplasm / cytoskeleton organization / centriole / sarcomere / axonogenesis / mitotic spindle organization / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / kinetochore / spindle pole / spindle / actin filament binding / actin cytoskeleton / nuclear envelope / actin binding / cell cortex / midbody / actin cytoskeleton organization / microtubule / cytoskeleton / hydrolase activity / cell division / axon / focal adhesion / centrosome / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Lau CK / Lacey SE | |||||||||
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 | 28.9 KB 28.9 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 | |
Filedesc metadata | emd-11313.cif.gz | 8.8 KB | ||
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 |
-Validation report
Summary document | emd_11313_validation.pdf.gz | 780.3 KB | Display | EMDB validaton report |
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Full document | emd_11313_full_validation.pdf.gz | 779.9 KB | Display | |
Data in XML | emd_11313_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | emd_11313_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11313 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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: |