[English] 日本語
Yorodumi- PDB-5cxl: CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cxl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS | |||||||||
Components | Bifunctional hemolysin/adenylate cyclase | |||||||||
Keywords | TOXIN / ADENYLATE CYCLASE / RTX MOTIFS / CALCIUM BINDING | |||||||||
Function / homology | Function and homology information calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding ...calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Bordetella pertussis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Motlova, L. / Barinka, C. / Bumba, L. | |||||||||
Funding support | Czech Republic, 2items
| |||||||||
Citation | Journal: Mol Cell / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cxl.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cxl.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cxl_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5cxl_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 5cxl_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5cxl_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxl ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxl | HTTPS FTP |
-Related structure data
Related structure data | 5cvwSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16024.102 Da / Num. of mol.: 2 / Fragment: BLOCK V OF RTX DOMAIN (UNP RESISDUES 1529-1681) Source method: isolated from a genetically manipulated source Details: THE LAST 5 AMINO ACIDS ARE TOO FLEXIBLE TO BE FIT IN THE ELECTRON DENSITY MAP. Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria) Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: cya, cyaA, BP0760 / Plasmid: PET42B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DKX7, adenylate cyclase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.99 % / Description: COLOURLESS, CUBE (a=100 um) |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting 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 NITRATE, 20% V/V PEG 3350, PH range: 7 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
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: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 46709 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.55 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.11 |
Reflection shell | Resolution: 1.45→1.54 Å / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.55 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5CVW Resolution: 1.45→32.15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.655 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: USED WEIGHTING FACTOR 2.5 AND ANISOTROPIC THERMAL FACTORS WERE REFINED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→32.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|