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- 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
TitleCrystal structure of FimH A27V/V163A from E. coli UTI89 bound to FimG N-terminal extension
Components
  • FimG N-terminal extension
  • Type 1 fimbiral adhesin FimH
KeywordsSUGAR 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 / metal ion binding
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type 1 fimbiral adhesin FimH / Type 1 fimbriae minor subunit FimG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsKalas, V. / Hultgren, S.J.
CitationJournal: 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
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Derived calculations
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type 1 fimbiral adhesin FimH
B: FimG N-terminal extension
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6834
Polymers30,5512
Non-polymers1322
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-20 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.320, 33.030, 72.450
Angle α, β, γ (deg.)90.00, 120.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Type 1 fimbiral adhesin FimH


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
#2: Protein/peptide FimG N-terminal extension


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 / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.59→2.73 Å / Redundancy: 6 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KLF

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
RfactorNum. reflection% reflection
Rfree0.2632 404 5.08 %
Rwork0.2145 --
obs0.217 7954 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.596→62.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 7 24 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032189
X-RAY DIFFRACTIONf_angle_d0.6583004
X-RAY DIFFRACTIONf_dihedral_angle_d11.597743
X-RAY DIFFRACTIONf_chiral_restr0.026363
X-RAY DIFFRACTIONf_plane_restr0.003390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5955-2.97110.32361220.26982476X-RAY DIFFRACTION99
2.9711-3.74320.2571410.2212491X-RAY DIFFRACTION100
3.7432-62.36580.24481410.18792583X-RAY DIFFRACTION100

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