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Yorodumi- PDB-5jr4: Crystal structure of FimH A27V/V163A from E. coli UTI89 bound to ... -
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-Basic information
Entry | Database: PDB / ID: 5jr4 | ||||||
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Title | Crystal structure of FimH A27V/V163A from E. coli UTI89 bound to FimG N-terminal extension | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / lectin / immunoglobulin fold / carbohydrate binding protein / donor strand exchange | ||||||
Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / cell adhesion Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.596 Å | ||||||
Authors | Kalas, V. / Hultgren, S.J. | ||||||
Citation | Journal: Sci Adv / Year: 2017 Title: Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions. Authors: Vasilios Kalas / Jerome S Pinkner / Thomas J Hannan / Michael E Hibbing / Karen W Dodson / Alex S Holehouse / Hao Zhang / Niraj H Tolia / Michael L Gross / Rohit V Pappu / James Janetka / Scott J Hultgren / Abstract: Positive selection in the two-domain type 1 pilus adhesin FimH enhances fitness in urinary tract infection (UTI). We report a comprehensive atomic-level view of FimH in two-state conformational ...Positive selection in the two-domain type 1 pilus adhesin FimH enhances fitness in urinary tract infection (UTI). We report a comprehensive atomic-level view of FimH in two-state conformational ensembles in solution, composed of one low-affinity tense (T) and multiple high-affinity relaxed (R) conformations. Positively selected residues allosterically modulate the equilibrium between these two conformational states, each of which engages mannose through distinct binding orientations. A FimH variant that only adopts the R state is severely attenuated early in a mouse model of uncomplicated UTI but is proficient at colonizing catheterized bladders in vivo or bladder transitional-like epithelial cells in vitro. Thus, the bladder habitat has barrier(s) to R state-mediated colonization possibly conferred by the terminally differentiated bladder epithelium and/or decoy receptors in urine. Together, our studies reveal the conformational landscape in solution, binding mechanisms, and adhesive strength of an allosteric two-domain adhesin that evolved "moderate" affinity to optimize persistence in the bladder during UTI. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jr4.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jr4.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jr4_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 5jr4_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 5jr4_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5jr4_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/5jr4 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/5jr4 | HTTPS FTP |
-Related structure data
Related structure data | 5jqiC 1klfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29037.260 Da / Num. of mol.: 1 / Fragment: UNP residues 22-300 / Mutation: A27V, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain UTI89 / UPEC) (bacteria) Strain: UTI89 / UPEC / Gene: fimH, UTI89_C5017 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2J4 |
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#2: Protein/peptide | Mass: 1513.776 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Escherichia coli (strain UTI89 / UPEC) (bacteria) References: UniProt: Q1R2J5*PLUS |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M MES pH 5.6, 0.2 M Calcium Acetate, 5% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→62.35 Å / Num. obs: 7964 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 6 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.3 / % possible all: 95.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KLF Resolution: 2.596→62.348 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.596→62.348 Å
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Refine LS restraints |
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LS refinement shell |
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