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Yorodumi- PDB-7pdz: Structure of capping protein bound to the barbed end of a cytopla... -
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-Basic information
Entry | Database: PDB / ID: 7pdz | ||||||
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Title | Structure of capping protein bound to the barbed end of a cytoplasmic actin filament | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Cytoskeleton / cell-shape remodelling / barbed end | ||||||
Function / homology | Function and homology information cytoskeletal calyx / : / Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / RHOD GTPase cycle / Gap junction degradation / Formation of annular gap junctions ...cytoskeletal calyx / : / Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / RHOD GTPase cycle / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / RHOF GTPase cycle / EPHB-mediated forward signaling / COPI-independent Golgi-to-ER retrograde traffic / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / RHO GTPases Activate Formins / F-actin capping protein complex / WASH complex / COPI-mediated anterograde transport / DNA Damage Recognition in GG-NER / negative regulation of filopodium assembly / UCH proteinases / VEGFA-VEGFR2 Pathway / structural constituent of postsynaptic actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / dense body / Clathrin-mediated endocytosis / 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 / lamellipodium assembly / cortical cytoskeleton / NuA4 histone acetyltransferase complex / brush border / asymmetric synapse / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / axonogenesis / actin filament / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / Schaffer collateral - CA1 synapse / Z disc / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / actin cytoskeleton organization / dendritic spine / postsynaptic density / cytoskeleton / hydrolase activity / axon / focal adhesion / neuronal cell body / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Bos taurus (cattle) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Funk, J. / Merino, F. / Schacks, M. / Rottner, K. / Raunser, S. / Bieling, P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks. Authors: Johanna Funk / Felipe Merino / Matthias Schaks / Klemens Rottner / Stefan Raunser / Peter Bieling / Abstract: Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside ...Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside from terminating filament growth, CP potentiates the nucleation of actin filaments by the Arp2/3 complex in branched actin networks through an unclear mechanism. Here, we combine structural biology with in vitro reconstitution to demonstrate that CP not only terminates filament elongation, but indirectly stimulates the activity of Arp2/3 activating nucleation promoting factors (NPFs) by preventing their association to filament barbed ends. Key to this function is one of CP's C-terminal "tentacle" extensions, which sterically masks the main interaction site of the terminal actin protomer. Deletion of the β tentacle only modestly impairs capping. However, in the context of a growing branched actin network, its removal potently inhibits nucleation promoting factors by tethering them to capped filament ends. End tethering of NPFs prevents their loading with actin monomers required for activation of the Arp2/3 complex and thus strongly inhibits branched network assembly both in cells and reconstituted motility assays. Our results mechanistically explain how CP couples two opposed processes-capping and nucleation-in branched actin network assembly. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7pdz.cif.gz | 481.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pdz.ent.gz | 410.6 KB | Display | PDB format |
PDBx/mmJSON format | 7pdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pdz_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7pdz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7pdz_validation.xml.gz | 87.2 KB | Display | |
Data in CIF | 7pdz_validation.cif.gz | 123.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/7pdz ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pdz | HTTPS FTP |
-Related structure data
Related structure data | 13343MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 8 molecules EFIJKLNO
#1: 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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#2: 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 |
#3: Protein | Mass: 41795.680 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P60712 |
-Protein/peptide , 1 types, 5 molecules QRSTP
#4: Protein/peptide |
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-Non-polymers , 3 types, 16 molecules
#5: Chemical | ChemComp-ADP / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-PO4 / |
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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
Component | Name: Complex between capping protein and the barbed end of cytoplasmic actin filaments Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Buffer solution | pH: 7 / Details: KMEI buffer | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: Mild discharging with 5 mA current / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3 sec. / Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4204 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 570724 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60206 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 40 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5ADX |