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Yorodumi- EMDB-17558: Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleate... -
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Basic information
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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 informationcytoskeletal calyx / regulation of protein kinase C signaling / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / lamellipodium organization / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / spindle localization ...cytoskeletal calyx / regulation of protein kinase C signaling / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / lamellipodium organization / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / spindle localization / meiotic cytokinesis / RHOD GTPase cycle / actin polymerization-dependent cell motility / 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 / COPI-independent Golgi-to-ER retrograde traffic / UCH proteinases / muscle cell projection membrane / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / asymmetric cell division / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin nucleation / COPI-mediated anterograde transport / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / Arp2/3 complex binding / mitotic spindle midzone / regulation of cell projection assembly / actin cap / sperm head / modification of postsynaptic actin cytoskeleton / regulation of mitophagy / positive regulation of smooth muscle contraction / profilin binding / Factors involved in megakaryocyte development and platelet production / cellular response to cytochalasin B / regulation of actin filament polymerization / substrate-dependent cell migration, cell extension / regulation of transepithelial transport / positive regulation of chemotaxis / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / cell junction assembly / barbed-end actin filament capping / focal adhesion assembly / protein localization to adherens junction / MHC class II antigen presentation / dense body / actin polymerization or depolymerization / Tat protein binding / cell projection organization / postsynaptic actin cytoskeleton / muscle cell development / proline-rich region binding / regulation of cell morphogenesis / adherens junction assembly / apical protein localization / dendritic spine maintenance / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / tight junction / podosome / regulation of axon extension / lamellipodium assembly / apical junction complex / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / transporter regulator activity / nitric-oxide synthase binding / cortical cytoskeleton / positive regulation of actin filament polymerization / filamentous actin / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / brush border / asymmetric synapse / intercalated disc / cilium assembly / kinesin binding / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / beta-tubulin binding / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / neuron projection morphogenesis / extrinsic apoptotic signaling pathway / ruffle Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() ![]() 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: 2024Title: 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. | |||||||||
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Structure visualization
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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 ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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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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-Half map: #1
| File | emd_17558_half_map_2.map | ||||||||||||
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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 |
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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. |
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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 |
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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: |
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About Yorodumi



Keywords
Homo sapiens (human)
Amanita phalloides (death cap)
Authors
Citation





















Z (Sec.)
Y (Row.)
X (Col.)




































unidentified baculovirus

FIELD EMISSION GUN

