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Yorodumi- PDB-4hji: Structure of the CooA pilin subunit from enterotoxigenic Escheric... -
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-Basic information
Entry | Database: PDB / ID: 4hji | ||||||
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Title | Structure of the CooA pilin subunit from enterotoxigenic Escherichia coli | ||||||
Components | CS1 fimbrial subunit A | ||||||
Keywords | CELL ADHESION / CS1 pilus / COLONIZATION FACTOR / pilin / chaperone-usher family / BACTERIAL SURFACE | ||||||
Function / homology | CFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE / CS1 fimbrial subunit A Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kolappan, S. / Zong, Z. / Craig, L. | ||||||
Citation | Journal: J Bacteriol / Year: 2013 Title: The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism. Authors: Vitold E Galkin / Subramaniapillai Kolappan / Dixon Ng / ZuSheng Zong / Juliana Li / Xiong Yu / Edward H Egelman / Lisa Craig / Abstract: Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine ...Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine via a variety of different pili. The CS1 pilus is a prototype for a family of related pili, including the CFA/I pili, present on ETEC and other Gram-negative bacterial pathogens. These pili are assembled by an outer membrane usher protein that catalyzes subunit polymerization via donor strand complementation, in which the N terminus of each incoming pilin subunit fits into a hydrophobic groove in the terminal subunit, completing a β-sheet in the Ig fold. Here we determined a crystal structure of the CS1 major pilin subunit, CooA, to a 1.6-Å resolution. CooA is a globular protein with an Ig fold and is similar in structure to the CFA/I major pilin CfaB. We determined three distinct negative-stain electron microscopic reconstructions of the CS1 pilus and generated pseudoatomic-resolution pilus structures using the CooA crystal structure. CS1 pili adopt multiple structural states with differences in subunit orientations and packing. We propose that the structural perturbations are accommodated by flexibility in the N-terminal donor strand of CooA and by plasticity in interactions between exposed flexible loops on adjacent subunits. Our results suggest that CS1 and other pili of this class are extensible filaments that can be stretched in response to mechanical stress encountered during colonization. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hji.cif.gz | 130 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hji.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/4hji ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hji | HTTPS FTP |
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-Related structure data
Related structure data | 1951C 1952C 1953C 3f83S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18245.250 Da / Num. of mol.: 2 / Fragment: CS1 PILIN, COOA-DSE: unp residues 35-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: LMC10 / Gene: csoA, cooA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABW7 #2: Chemical | ChemComp-IMD / | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1 M SODIUM CITRATE, 100 MM IMIDAZOLE , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.07 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 8, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 131428 / Num. obs: 33503 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.47 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 1.6→1.69 Å / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F83 Resolution: 1.6→19.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.108 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.257 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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