+Open data
-Basic information
Entry | Database: PDB / ID: 7p1h | ||||||
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Title | Structure of the V. vulnificus ExoY-G-actin-profilin complex | ||||||
Components |
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Keywords | TOXIN / Bacterial toxin / G-actin / profilin | ||||||
Function / homology | Function and homology information calcium- and calmodulin-responsive adenylate cyclase activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / synapse maturation / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex ...calcium- and calmodulin-responsive adenylate cyclase activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / synapse maturation / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Signaling by ROBO receptors / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of actin filament polymerization / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / positive regulation of ruffle assembly / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / negative regulation of stress fiber assembly / host cell cytosol / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of actin filament polymerization / positive regulation of stem cell population maintenance / detection of maltose stimulus / NuA4 histone acetyltransferase complex / maltose transport complex / nitric-oxide synthase binding / positive regulation of epithelial cell migration / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / carbohydrate transport / brush border / calyx of Held / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / positive regulation of double-strand break repair via homologous recombination / : / maltose binding / actin monomer binding / 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 / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / ATP-binding cassette (ABC) transporter complex / axonogenesis / cell chemotaxis / negative regulation of protein binding / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Vibrio vulnificus (bacteria) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Belyy, A. / Merino, F. / Raunser, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2021 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. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7p1h.cif.gz | 308.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p1h.ent.gz | 252 KB | Display | PDB format |
PDBx/mmJSON format | 7p1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p1h_validation.pdf.gz | 604.4 KB | Display | wwPDB validaton report |
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Full document | 7p1h_full_validation.pdf.gz | 616.8 KB | Display | |
Data in XML | 7p1h_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 7p1h_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/7p1h ftp://data.pdbj.org/pub/pdb/validation_reports/p1/7p1h | HTTPS FTP |
-Related structure data
Related structure data | 13159MC 7p1gC 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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-Components
#1: Protein | Mass: 91467.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Vibrio vulnificus (bacteria) Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: P0AEX9, UniProt: A0A0F6NGV0 |
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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.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60709 |
#3: Protein | Mass: 15071.222 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07737 |
#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 |
-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 % |
-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: SPOT SCAN |
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 |
-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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