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- PDB-6gtv: Crystal structure of a FimH*DsG complex from E.coli F18 with boun... -

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Basic information

Entry
Database: PDB / ID: 6gtv
TitleCrystal structure of a FimH*DsG complex from E.coli F18 with bound trimannose
Components
  • FimG protein
  • FimH protein
KeywordsCELL ADHESION / TYPE I PILUS / CATCH-BOND / LECTIN / UPEC / INFECTION / MANNOSE
Function / homology
Function and homology information


pilus / cell adhesion
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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / FimH protein / FimG protein
Similarity search - Component
Biological speciesEscherichia coli F18+ (bacteria)
Escherichia coli 536 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJakob, R.P. / Sauer, M.M. / Luber, T. / Canonica, F. / Navarra, G. / Ernst, B. / Unverzagt, C. / Maier, T. / Glockshuber, R.
CitationJournal: J Am Chem Soc / Year: 2019
Title: Binding of the Bacterial Adhesin FimH to Its Natural, Multivalent High-Mannose Type Glycan Targets.
Authors: Maximilian M Sauer / Roman P Jakob / Thomas Luber / Fabia Canonica / Giulio Navarra / Beat Ernst / Carlo Unverzagt / Timm Maier / Rudi Glockshuber /
Abstract: Multivalent carbohydrate-lectin interactions at host-pathogen interfaces play a crucial role in the establishment of infections. Although competitive antagonists that prevent pathogen adhesion are ...Multivalent carbohydrate-lectin interactions at host-pathogen interfaces play a crucial role in the establishment of infections. Although competitive antagonists that prevent pathogen adhesion are promising antimicrobial drugs, the molecular mechanisms underlying these complex adhesion processes are still poorly understood. Here, we characterize the interactions between the fimbrial adhesin FimH from uropathogenic Escherichia coli strains and its natural high-mannose type N-glycan binding epitopes on uroepithelial glycoproteins. Crystal structures and a detailed kinetic characterization of ligand-binding and dissociation revealed that the binding pocket of FimH evolved such that it recognizes the terminal α(1-2)-, α(1-3)-, and α(1-6)-linked mannosides of natural high-mannose type N-glycans with similar affinity. We demonstrate that the 2000-fold higher affinity of the domain-separated state of FimH compared to its domain-associated state is ligand-independent and consistent with a thermodynamic cycle in which ligand-binding shifts the association equilibrium between the FimH lectin and the FimH pilin domain. Moreover, we show that a single N-glycan can bind up to three molecules of FimH, albeit with negative cooperativity, so that a molar excess of accessible N-glycans over FimH on the cell surface favors monovalent FimH binding. Our data provide pivotal insights into the adhesion properties of uropathogenic Escherichia coli strains to their target receptors and a solid basis for the development of effective FimH antagonists.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FimH protein
B: FimG protein
C: FimH protein
D: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,21311
Polymers60,9404
Non-polymers1,2737
Water8,233457
1
A: FimH protein
B: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0276
Polymers30,4702
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint1 kcal/mol
Surface area13210 Å2
MethodPISA
2
C: FimH protein
D: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1875
Polymers30,4702
Non-polymers7173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint1 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.690, 119.210, 120.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules ACBD

#1: Protein FimH protein


Mass: 29053.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli F18+ (bacteria) / Gene: ECP_4655, fimh / Plasmid: pTRC99a / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: A0A0R4I961
#2: Protein/peptide FimG protein


Mass: 1416.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli 536 (bacteria) / References: UniProt: A0A140UH97
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 463 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 0.1 M Hepes pH 7.5, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.1→48.727 Å / Num. obs: 49075 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rrim(I) all: 0.106 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7428 / CC1/2: 0.729 / Rrim(I) all: 1.151 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOE

4xoe


Resolution: 2.1→48.727 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.55
RfactorNum. reflection% reflection
Rfree0.2172 2483 5.06 %
Rwork0.1877 --
obs0.1892 49075 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 85 457 4820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044461
X-RAY DIFFRACTIONf_angle_d0.8326114
X-RAY DIFFRACTIONf_dihedral_angle_d13.1942616
X-RAY DIFFRACTIONf_chiral_restr0.118742
X-RAY DIFFRACTIONf_plane_restr0.004782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.14030.34521420.3212552X-RAY DIFFRACTION99
2.1403-2.1840.30781260.28432576X-RAY DIFFRACTION100
2.184-2.23150.30941370.2672524X-RAY DIFFRACTION100
2.2315-2.28340.27721370.23882573X-RAY DIFFRACTION100
2.2834-2.34050.24261390.2352552X-RAY DIFFRACTION100
2.3405-2.40380.2731460.23662556X-RAY DIFFRACTION100
2.4038-2.47450.26471500.22722565X-RAY DIFFRACTION100
2.4745-2.55440.26231390.22312552X-RAY DIFFRACTION100
2.5544-2.64570.2541210.20952582X-RAY DIFFRACTION100
2.6457-2.75160.25191370.20042588X-RAY DIFFRACTION100
2.7516-2.87680.25881390.19072570X-RAY DIFFRACTION100
2.8768-3.02850.23881350.1932588X-RAY DIFFRACTION100
3.0285-3.21820.23311210.19052604X-RAY DIFFRACTION100
3.2182-3.46660.19461630.18082578X-RAY DIFFRACTION100
3.4666-3.81530.20391400.16782604X-RAY DIFFRACTION100
3.8153-4.36710.1881430.1592622X-RAY DIFFRACTION100
4.3671-5.50090.151280.13692649X-RAY DIFFRACTION100
5.5009-48.74030.2151400.19712757X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32840.3119-0.6785-0.0591-0.23571.1844-0.0560.0546-0.0027-0.00390.0625-0.00670.0439-0.139-00.3935-0.001-0.03350.37440.02470.3896128.5535129.2089-1.8024
20.51010.24450.2540.4083-0.38510.6425-0.0583-0.1090.03350.1826-0.1734-0.0899-0.53830.4258-0.00010.429-0.0562-0.06630.41130.02140.4293135.8974136.75625.6878
30.24030.1556-0.21640.4273-0.55640.6009-0.20940.15710.2073-0.0146-0.0340.1565-0.05470.262-0.00570.4158-0.0355-0.06080.41950.05060.4185135.5191133.806-6.0653
40.3577-0.06080.51020.35870.20480.66-0.0041-0.10450.0660.0854-0.11790.0231-0.38690.1695-00.3969-0.0096-0.05520.41570.03980.4024131.2444132.683810.2167
50.1503-0.0980.16380.11950.15460.61980.0271-0.00720.00120.0066-0.04750.1002-0.20950.180700.37050.0223-0.03220.39550.03250.4083127.3195124.86813.9479
60.55240.13550.42640.6407-0.55770.78120.0245-0.14770.02290.0716-0.077-0.02350.00060.1903-00.35270.0311-0.0120.40580.0220.3778131.7941114.073238.6273
70.4793-0.5020.06290.46150.11810.3929-0.2194-0.14080.15730.00510.22630.30310.1389-0.127300.4070.0261-0.00490.42110.05230.4308122.5007111.366736.8132
80.2828-0.3556-0.42751.2937-0.75760.70580.0450.15530.0938-0.0711-0.297-0.2514-0.04190.2097-00.49990.0287-0.04090.44110.10730.4733111.3474147.9333-34.8661
90.5002-0.50480.07580.3843-0.18090.3221-0.33930.06240.20530.45940.1319-0.2233-0.853-0.1111-0.00240.72130.0597-0.1350.47380.09310.5215106.2927159.1814-31.0671
100.3285-0.02180.45330.2107-0.3471.0522-0.1812-0.11920.06610.17120.0687-0.128-0.34060.0028-00.59090.0428-0.09170.43610.06770.5198108.9283148.685-25.9137
110.7804-0.3113-0.30320.9794-0.51480.2478-0.06520.28230.3240.3399-0.382-0.4449-0.47950.324-0.00010.5525-0.0299-0.14630.40840.14580.5541111.6423156.5095-34.306
121.0118-0.28960.62821.2835-0.5690.69840.06810.0377-0.19730.1236-0.11830.07780.20720.250500.42590.0601-0.05230.41080.06130.432593.3689161.9937-59.3457
130.2116-0.25030.41620.6209-0.00231.24430.31570.18470.3730.0882-0.2544-0.0463-0.30070.1661-0.00020.45550.1027-0.00120.55250.080.423593.0114172.5949-72.5065
140.5084-0.03590.47340.7967-0.49810.46260.15140.08-0.11770.1082-0.10880.00410.23080.15290.00020.36320.0644-0.04370.40820.04510.404890.4537167.2515-66.8474
150.29840.4521-0.15220.4423-0.1720.06750.3368-0.0297-0.24480.07370.2371-0.28230.29280.74360.00040.56540.1953-0.00660.5353-0.0010.486298.1302164.1426-71.9768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 135 )
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 279 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 14 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 53 )
9X-RAY DIFFRACTION9chain 'C' and (resid 54 through 84 )
10X-RAY DIFFRACTION10chain 'C' and (resid 85 through 104 )
11X-RAY DIFFRACTION11chain 'C' and (resid 105 through 150 )
12X-RAY DIFFRACTION12chain 'C' and (resid 151 through 198 )
13X-RAY DIFFRACTION13chain 'C' and (resid 199 through 237 )
14X-RAY DIFFRACTION14chain 'C' and (resid 238 through 279 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 14 )

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