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Yorodumi- PDB-8p94: Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p94 | ||||||
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Title | Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / Complex | ||||||
Function / homology | Function and homology information cytoskeletal calyx / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / meiotic cytokinesis / muscle cell projection membrane / RHOF GTPase cycle / lamellipodium organization / Advanced glycosylation endproduct receptor signaling ...cytoskeletal calyx / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / meiotic cytokinesis / muscle cell projection membrane / RHOF GTPase cycle / lamellipodium organization / Advanced glycosylation endproduct receptor signaling / 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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / site of polarized growth / actin polymerization-dependent cell motility / COPI-independent Golgi-to-ER retrograde traffic / Clathrin-mediated endocytosis / Arp2/3 protein complex / asymmetric cell division / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Arp2/3 complex-mediated actin nucleation / actin nucleation / WASH complex / Arp2/3 complex binding / sperm connecting piece / F-actin capping protein complex / COPI-mediated anterograde transport / negative regulation of filopodium assembly / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / cellular response to cytochalasin B / actin cap / regulation of mitophagy / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / profilin binding / substrate-dependent cell migration, cell extension / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Factors involved in megakaryocyte development and platelet production / Tat protein binding / positive regulation of smooth muscle contraction / positive regulation of chemotaxis / regulation of actin filament polymerization / cell projection organization / cell junction assembly / apical protein localization / MHC class II antigen presentation / barbed-end actin filament capping / actin polymerization or depolymerization / adherens junction assembly / focal adhesion assembly / podosome / RHO GTPases activate IQGAPs / regulation of cell morphogenesis / RHO GTPases Activate Formins / regulation of lamellipodium assembly / regulation of axon extension / proline-rich region binding / tight junction / regulation of norepinephrine uptake / NuA4 histone acetyltransferase complex / lamellipodium assembly / dendritic spine maintenance / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of actin filament polymerization / nitric-oxide synthase binding / filamentous actin / brush border / kinesin binding / calyx of Held / cilium assembly / asymmetric synapse / RHO GTPases Activate WASPs and WAVEs / regulation of protein localization to plasma membrane / voltage-gated potassium channel complex / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / extrinsic apoptotic signaling pathway / clathrin-coated pit / ruffle / EPHB-mediated forward signaling / hippocampal mossy fiber to CA3 synapse Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) Sus scrofa (pig) Amanita phalloides (death cap) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Liu, T. / Moores, C.A. | ||||||
Funding support | European Union, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p94.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8p94.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/8p94 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/8p94 | HTTPS FTP |
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-Related structure data
Related structure data | 17558MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Actin-related protein ... , 7 types, 7 molecules ABCDEFG
#1: Protein | Mass: 47428.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR3, ARP3 / Production host: unidentified baculovirus / References: UniProt: P61158 |
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#2: Protein | Mass: 44818.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR2, ARP2 / Production host: unidentified baculovirus / References: UniProt: P61160 |
#3: Protein | Mass: 41004.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC1B, ARC41 / Production host: unidentified baculovirus / References: UniProt: O15143 |
#4: Protein | Mass: 34386.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC2, ARC34, PRO2446 / Production host: unidentified baculovirus / References: UniProt: O15144 |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC3, ARC21 / Production host: unidentified baculovirus / References: UniProt: O15145 |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC4, ARC20 / Production host: unidentified baculovirus / References: UniProt: P59998 |
#7: Protein | Mass: 16964.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC5L / Production host: unidentified baculovirus / References: UniProt: Q9BPX5 |
-Protein , 4 types, 13 molecules HJKNOPQRSWIUV
#8: Protein | Mass: 41782.660 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1 #9: Protein | | Mass: 61340.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60598 #10: Protein | | Mass: 32980.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capza1, Cappa1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47753 #11: Protein | | Mass: 30669.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capzb, Cappb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47757 |
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-Protein/peptide , 1 types, 10 molecules abcdhijklm
#12: Protein/peptide | Type: Peptide-like / Class: Toxin / Mass: 808.899 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Amanita phalloides (death cap) / References: BIRD: PRD_002366 |
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-Non-polymers , 2 types, 24 molecules
#13: Chemical | ChemComp-ADP / #14: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 Details: 20 mM HEPES pH 7.5, 50mM KCl, 1mM EGTA, 1mM MgCl2, 0.2 mM ATP and 1 mM DTT | ||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 295.15 K / Details: Back blotting |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Details: CryoSPARC Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2001580 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130915 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building |
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