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Open data
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Basic information
Entry | Database: PDB / ID: 7p1h | ||||||
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Title | Structure of the V. vulnificus ExoY-G-actin-profilin complex | ||||||
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![]() | TOXIN / Bacterial toxin / G-actin / profilin | ||||||
Function / homology | ![]() calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / regulation of transepithelial transport / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / regulation of transepithelial transport / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / Signaling by ROBO receptors / Gap junction degradation / regulation of actin filament polymerization / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of ATP-dependent activity / Adherens junctions interactions / tight junction / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / negative regulation of stress fiber assembly / positive regulation of T cell differentiation / apical junction complex / host cell cytosol / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of actin filament polymerization / detection of maltose stimulus / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of stem cell population maintenance / maltose transport complex / positive regulation of epithelial cell migration / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / carbohydrate transport / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / : / actin monomer binding / maltose binding / positive regulation of double-strand break repair via homologous recombination / maltose transport / maltodextrin transmembrane transport / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / EPHB-mediated forward signaling / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / phosphotyrosine residue binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / axonogenesis / negative regulation of protein binding / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Belyy, A. / Merino, F. / Raunser, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens. Authors: Alexander Belyy / Felipe Merino / Undine Mechold / Stefan Raunser / ![]() ![]() Abstract: Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this ...Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this activation is, however, unclear. Here, we report structures of ExoY from Pseudomonas aeruginosa and Vibrio vulnificus bound to their corresponding activators F-actin and profilin-G-actin. The structures reveal that in contrast to the apo-state, two flexible regions become ordered and interact strongly with actin. The specific stabilization of these regions results in an allosteric stabilization of the nucleotide binding pocket and thereby to an activation of the enzyme. Differences in the sequence and conformation of the actin-binding regions are responsible for the selective binding to either F- or G-actin. Other nucleotidyl cyclase toxins that bind to calmodulin rather than actin undergo a similar disordered-to-ordered transition during activation, suggesting that the allosteric activation-by-stabilization mechanism of ExoY is conserved in these enzymes, albeit the different activator. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 252 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 13159MC ![]() 7p1gC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 91467.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994 / Production host: ![]() ![]() |
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#2: Protein | Mass: 41402.242 Da / Num. of mol.: 1 / Mutation: C272A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 15071.222 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-ATP / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Structure of the V. vulnificus ExoY-G-actin-profilin complex Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Average exposure time: 2 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6879 |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1252333 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 342081 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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