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- PDB-5jqi: Crystal structure of FimH A62S from E. coli UTI89 bound to FimG N... -

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Basic information

Entry
Database: PDB / ID: 5jqi
TitleCrystal structure of FimH A62S 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)
Escherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.962 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 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 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 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
G: FimG N-terminal extension
H: Type 1 fimbiral adhesin FimH
A: FimG N-terminal extension
B: Type 1 fimbiral adhesin FimH
C: FimG N-terminal extension
D: Type 1 fimbiral adhesin FimH
E: FimG N-terminal extension
F: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,63712
Polymers122,2688
Non-polymers3684
Water16,033890
1
G: FimG N-terminal extension
H: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10 kcal/mol
Surface area13130 Å2
MethodPISA
2
A: FimG N-terminal extension
B: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area13280 Å2
MethodPISA
3
C: FimG N-terminal extension
D: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10 kcal/mol
Surface area12980 Å2
MethodPISA
4
E: FimG N-terminal extension
F: Type 1 fimbiral adhesin FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6593
Polymers30,5672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.440, 75.560, 78.440
Angle α, β, γ (deg.)68.35, 69.00, 77.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
FimG N-terminal extension


Mass: 1513.776 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli UTI89 (bacteria) / References: UniProt: Q1R2J5*PLUS
#2: Protein
Type 1 fimbiral adhesin FimH


Mass: 29053.260 Da / Num. of mol.: 4 / Fragment: UNP residues 22-300 / Mutation: A62S
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium Acetate, 0.1 M HEPES 7.5, 10% PEG 8000
PH range: 5-8

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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: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.96→48.67 Å / Num. obs: 75411 / % possible obs: 94.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.5
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JWN

3jwn


Resolution: 1.962→48.666 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2394 3735 4.95 %
Rwork0.1888 --
obs0.1913 75394 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.962→48.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8491 0 24 890 9405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048724
X-RAY DIFFRACTIONf_angle_d0.7911966
X-RAY DIFFRACTIONf_dihedral_angle_d11.0072962
X-RAY DIFFRACTIONf_chiral_restr0.0311448
X-RAY DIFFRACTIONf_plane_restr0.0041548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9621-1.98690.31741360.30312389X-RAY DIFFRACTION87
1.9869-2.0130.3241380.24562618X-RAY DIFFRACTION91
2.013-2.04060.31491270.24492556X-RAY DIFFRACTION92
2.0406-2.06980.30231420.23542593X-RAY DIFFRACTION92
2.0698-2.10070.31641430.24072584X-RAY DIFFRACTION92
2.1007-2.13350.31061400.24212550X-RAY DIFFRACTION92
2.1335-2.16850.28221410.23042642X-RAY DIFFRACTION93
2.1685-2.20590.31681450.22392585X-RAY DIFFRACTION93
2.2059-2.2460.28081360.22072640X-RAY DIFFRACTION93
2.246-2.28920.31731350.22432621X-RAY DIFFRACTION93
2.2892-2.33590.2831310.22372663X-RAY DIFFRACTION93
2.3359-2.38670.2991340.21692579X-RAY DIFFRACTION94
2.3867-2.44220.28171150.21122744X-RAY DIFFRACTION94
2.4422-2.50330.24961270.20942600X-RAY DIFFRACTION94
2.5033-2.57090.25561610.20462653X-RAY DIFFRACTION95
2.5709-2.64660.26921400.20692655X-RAY DIFFRACTION94
2.6466-2.7320.2431290.19472702X-RAY DIFFRACTION95
2.732-2.82960.25791480.19842672X-RAY DIFFRACTION95
2.8296-2.94290.24541360.20132707X-RAY DIFFRACTION96
2.9429-3.07680.25241310.19542692X-RAY DIFFRACTION96
3.0768-3.2390.24251610.18982728X-RAY DIFFRACTION96
3.239-3.44190.21171460.16552692X-RAY DIFFRACTION96
3.4419-3.70760.20561430.17532731X-RAY DIFFRACTION97
3.7076-4.08050.17981430.15942753X-RAY DIFFRACTION97
4.0805-4.67060.17061250.13482776X-RAY DIFFRACTION98
4.6706-5.88280.17171320.13762761X-RAY DIFFRACTION98
5.8828-48.68140.18911500.15362773X-RAY DIFFRACTION98

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