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Yorodumi- EMDB-17558: Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleate... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17558 | |||||||||
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Title | Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches | |||||||||
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Keywords | Complex / CONTRACTILE PROTEIN | |||||||||
Function / homology | Function and homology information cytoskeletal calyx / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / muscle cell projection membrane / : / meiotic cytokinesis / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle ...cytoskeletal calyx / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / muscle cell projection membrane / : / meiotic cytokinesis / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / spindle localization / RHOD GTPase cycle / 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 / actin polymerization-dependent cell motility / COPI-independent Golgi-to-ER retrograde traffic / Arp2/3 protein complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / asymmetric cell division / Arp2/3 complex-mediated actin nucleation / icosahedral viral capsid / actin nucleation / F-actin capping protein complex / WASH complex / COPI-mediated anterograde transport / negative regulation of filopodium assembly / actin cap / structural constituent of postsynaptic actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / regulation of actin filament polymerization / dense body / cell projection organization / cell junction assembly / MHC class II antigen presentation / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / lamellipodium assembly / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cortical cytoskeleton / NuA4 histone acetyltransferase complex / filamentous actin / brush border / cilium assembly / positive regulation of double-strand break repair via homologous recombination / asymmetric synapse / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / EPHB-mediated forward signaling / actin filament polymerization / ribonucleoside triphosphate phosphatase activity / hippocampal mossy fiber to CA3 synapse / axonogenesis / cellular response to nerve growth factor stimulus / cell projection / actin filament / cell motility / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / Schaffer collateral - CA1 synapse / endocytosis involved in viral entry into host cell / structural constituent of cytoskeleton / cellular response to type II interferon / Regulation of actin dynamics for phagocytic cup formation / Z disc / response to estrogen / azurophil granule lumen / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / response to estradiol / Clathrin-mediated endocytosis / site of double-strand break / actin binding / cell cortex / actin cytoskeleton organization / ficolin-1-rich granule lumen / host cell cytoplasm / dendritic spine / postsynaptic density / cytoskeleton / viral protein processing Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) / Amanita phalloides (death cap) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Liu T / Moores CA | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament. Authors: Tianyang Liu / Luyan Cao / Miroslav Mladenov / Antoine Jegou / Michael Way / Carolyn A Moores / Abstract: Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane ...Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane trafficking. Cortactin is important for actin branch stabilization, but the mechanism by which this occurs is unclear. Given this, we determined the structure of vertebrate cortactin-stabilized Arp2/3 actin branches using cryogenic electron microscopy. We find that cortactin interacts with the new daughter filament nucleated by the Arp2/3 complex at the branch site, rather than the initial mother actin filament. Cortactin preferentially binds activated Arp3. It also stabilizes the F-actin-like interface of activated Arp3 with the first actin subunit of the new filament, and its central repeats extend along successive daughter-filament subunits. The preference of cortactin for activated Arp3 explains its retention at the actin branch and accounts for its synergy with other nucleation-promoting factors in regulating branched actin network dynamics. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17558.map.gz | 163.1 MB | EMDB map data format | |
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Header (meta data) | emd-17558-v30.xml emd-17558.xml | 34.6 KB 34.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17558_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_17558.png | 72 KB | ||
Filedesc metadata | emd-17558.cif.gz | 9.3 KB | ||
Others | emd_17558_half_map_1.map.gz emd_17558_half_map_2.map.gz | 301.6 MB 301.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17558 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17558 | HTTPS FTP |
-Validation report
Summary document | emd_17558_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17558_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17558_validation.xml.gz | 24 KB | Display | |
Data in CIF | emd_17558_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17558 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17558 | HTTPS FTP |
-Related structure data
Related structure data | 8p94MC C: citing same article (ref.) M: atomic model generated by this map |
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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_17558.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17558_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17558_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cortactin stabilizes Arp2/3-complex nucleated actin branches with...
+Supramolecule #1: Cortactin stabilizes Arp2/3-complex nucleated actin branches with...
+Supramolecule #2: Human Arp2/3 C1BC5L complex
+Supramolecule #3: Porcine actin, cytoplasmic 1
+Supramolecule #4: Mouse cortactin
+Supramolecule #5: Mouse capping protein
+Supramolecule #6: Phalloidin
+Macromolecule #1: Actin-related protein 3
+Macromolecule #2: Actin-related protein 2
+Macromolecule #3: Actin-related protein 2/3 complex subunit 1B
+Macromolecule #4: Actin-related protein 2/3 complex subunit 2
+Macromolecule #5: Actin-related protein 2/3 complex subunit 3
+Macromolecule #6: Actin-related protein 2/3 complex subunit 4
+Macromolecule #7: Actin-related protein 2/3 complex subunit 5-like protein
+Macromolecule #8: Actin, cytoplasmic 1
+Macromolecule #9: Src substrate cortactin
+Macromolecule #10: F-actin-capping protein subunit alpha-1
+Macromolecule #11: Isoform 2 of F-actin-capping protein subunit beta
+Macromolecule #12: Phalloidin
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 20 mM HEPES pH 7.5, 50mM KCl, 1mM EGTA, 1mM MgCl2, 0.2 mM ATP and 1 mM DTT |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP / Details: Back blotting. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: OTHER |
Output model | PDB-8p94: |