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- PDB-5cvw: CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cvw | |||||||||
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Title | CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS | |||||||||
![]() | Bifunctional hemolysin/adenylate cyclase | |||||||||
![]() | TOXIN / ADENYLATE CYCLASE / RTX MOTIFS / CALCIUM BINDING | |||||||||
Function / homology | ![]() calcium ion sequestering activity / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / ion binding / channel activity / toxin activity / calmodulin binding / calcium ion binding ...calcium ion sequestering activity / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / ion binding / channel activity / toxin activity / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Motlova, L. / Barinka, C. / Bumba, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Calcium-Driven Folding of RTX Domain β-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts. Authors: Ladislav Bumba / Jiri Masin / Pavel Macek / Tomas Wald / Lucia Motlova / Ilona Bibova / Nela Klimova / Lucie Bednarova / Vaclav Veverka / Michael Kachala / Dmitri I Svergun / Cyril Barinka / Peter Sebo / ![]() ![]() Abstract: Calcium-binding RTX proteins are equipped with C-terminal secretion signals and translocate from the Ca(2+)-depleted cytosol of Gram-negative bacteria directly into the Ca(2+)-rich external milieu, ...Calcium-binding RTX proteins are equipped with C-terminal secretion signals and translocate from the Ca(2+)-depleted cytosol of Gram-negative bacteria directly into the Ca(2+)-rich external milieu, passing through the "channel-tunnel" ducts of type I secretion systems (T1SSs). Using Bordetella pertussis adenylate cyclase toxin, we solved the structure of an essential C-terminal assembly that caps the RTX domains of RTX family leukotoxins. This is shown to scaffold directional Ca(2+)-dependent folding of the carboxy-proximal RTX repeat blocks into β-rolls. The resulting intramolecular Brownian ratchets then prevent backsliding of translocating RTX proteins in the T1SS conduits and thereby accelerate excretion of very large RTX leukotoxins from bacterial cells by a vectorial "push-ratchet" mechanism. Successive Ca(2+)-dependent and cosecretional acquisition of a functional RTX toxin structure in the course of T1SS-mediated translocation, through RTX domain folding from the C-terminal cap toward the N terminus, sets a paradigm that opens for design of virulence inhibitors of major pathogens. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 86.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 457.6 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cxlC ![]() 1srpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16024.102 Da / Num. of mol.: 1 / Fragment: BLOCK V OF RTX DOMAIN (UNP RESIDUES 1529-1681) Source method: isolated from a genetically manipulated source Details: The last 3 amino acids are too flexible to be fit in the electron density map. Source: (gene. exp.) ![]() Gene: cya, cyaA, BN118_0468 / Plasmid: PET42B / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 139 molecules ![](data/chem/img/CA.gif)
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![](data/chem/img/HOH.gif)
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % / Description: colourless, cube (a=90 um) |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Buffer composition: 5 mM Tris-HCl pH=7.4, 150 mM NaCl, 10 mM CaCl2 Precipitant composition: 0.2 M Magnesium sulfate, 20% v/v PEG 3350 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2012 / Details: 2 MIRRORS |
Radiation | Monochromator: Si-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→50 Å / Num. obs: 42131 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 4.48 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.78 |
Reflection shell | Resolution: 1.23→1.3 Å / % possible all: 72.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SRP Resolution: 1.25→29.24 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.507 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.732 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→29.24 Å
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Refine LS restraints |
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