+Open data
-Basic information
Entry | Database: PDB / ID: 7p1g | ||||||
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Title | Structure of the P. aeruginosa ExoY-F-actin complex | ||||||
Components |
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Keywords | TOXIN / Bacterial toxin / F-actin | ||||||
Function / homology | Function and homology information calcium- and calmodulin-responsive adenylate cyclase activity / cytoskeletal motor activator activity / detection of maltose stimulus / maltose transport complex / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle ...calcium- and calmodulin-responsive adenylate cyclase activity / cytoskeletal motor activator activity / detection of maltose stimulus / maltose transport complex / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / carbohydrate transport / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / carbohydrate transmembrane transporter activity / skeletal muscle myofibril / maltose binding / actin monomer binding / maltose transport / maltodextrin transmembrane transport / skeletal muscle fiber development / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / stress fiber / titin binding / actin filament polymerization / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / protein domain specific binding / DNA damage response / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular region / ATP binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Pseudomonas aeruginosa PAO1 (bacteria) Oryctolagus cuniculus (rabbit) Amanita phalloides (death cap) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7p1g.cif.gz | 662.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p1g.ent.gz | 536.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p1g_validation.pdf.gz | 747.7 KB | Display | wwPDB validaton report |
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Full document | 7p1g_full_validation.pdf.gz | 788.2 KB | Display | |
Data in XML | 7p1g_validation.xml.gz | 90.1 KB | Display | |
Data in CIF | 7p1g_validation.cif.gz | 132.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/7p1g ftp://data.pdbj.org/pub/pdb/validation_reports/p1/7p1g | HTTPS FTP |
-Related structure data
Related structure data | 13158MC 7p1hC 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 , 2 types, 10 molecules MKLNOCABDE
#1: Protein | Mass: 84941.797 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Gene: malE, b4034, JW3994, exoY, PA2191 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P0AEX9, UniProt: Q9I1S4 #2: Protein | Mass: 42096.953 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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-Protein/peptide , 1 types, 5 molecules HFGIJ
#3: Protein/peptide | Mass: 808.899 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Amanita phalloides (death cap) |
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-Non-polymers , 4 types, 25 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GH3 / #6: Chemical | ChemComp-ADP / #7: Chemical | ChemComp-PO4 / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The complex of P. aeruginosa ExoY with F-actin / 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: 3500 nm / Nominal defocus min: 400 nm |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 93 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12437 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2249589 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1535755 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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