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- PDB-6gu0: Crystal structure of a FimH*DsG complex from E.coli F18 with boun... -

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Basic information

Entry
Database: PDB / ID: 6gu0
TitleCrystal structure of a FimH*DsG complex from E.coli F18 with bound dimannoside Man(alpha1-3)Man in space group P213
Components
  • FimG protein
  • FimH protein
KeywordsCELL ADHESION / TYPE I PILUS / CATCH-BOND / LECTIN / UPEC / INFECTION / MANNOSE
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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli F18+ (bacteria)
Escherichia coli 536 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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
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
Revision 2.2Nov 13, 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: FimH protein
B: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9224
Polymers30,4702
Non-polymers4522
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, FimH and the FimG peptide form a stable complex via donor strand complementation, and together as FimH*DsG behave as monomeric complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-5 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.630, 128.630, 128.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein FimH protein


Mass: 29053.260 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli 536 (bacteria)
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M (NH4)2SO4, 0.1 M sodium cacodylate pH 6.5, 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.5→90.96 Å / Num. obs: 24813 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.998 / Rrim(I) all: 0.197 / Net I/σ(I): 17.9
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 20.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3918 / CC1/2: 0.684 / Rrim(I) all: 2.49 / % possible all: 99.9

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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: 2.501→64.315 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 1208 4.87 %RANDOM
Rwork0.1728 ---
obs0.1738 24813 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→64.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 29 232 2409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032223
X-RAY DIFFRACTIONf_angle_d0.6953057
X-RAY DIFFRACTIONf_dihedral_angle_d14.0751289
X-RAY DIFFRACTIONf_chiral_restr0.051374
X-RAY DIFFRACTIONf_plane_restr0.004391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5006-2.60070.32181250.32022603X-RAY DIFFRACTION100
2.6007-2.71910.31111000.26512640X-RAY DIFFRACTION100
2.7191-2.86250.28551390.25042586X-RAY DIFFRACTION100
2.8625-3.04180.24761310.20682586X-RAY DIFFRACTION100
3.0418-3.27670.20521570.1732571X-RAY DIFFRACTION100
3.2767-3.60640.18631460.15732610X-RAY DIFFRACTION100
3.6064-4.12810.19121130.14152651X-RAY DIFFRACTION100
4.1281-5.20070.1361270.12652651X-RAY DIFFRACTION100
5.2007-64.33630.17041700.17932707X-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)
10.2411-0.00910.06510.0502-0.03950.27570.23890.44910.1404-0.4341-0.2913-0.6133-0.3476-0.00110.00020.56580.01590.08580.38810.02390.443-5.2293-45.2359-3.177
20.26310.37110.63150.37060.4450.65750.01270.18350.2284-0.3212-0.13650.0675-0.3983-0.0765-0.00010.5440.03960.04440.3757-0.01280.5208-8.6766-37.501310.2
30.4694-0.2243-0.09651.61970.54520.24750.10040.0177-0.01080.1749-0.007-0.06070.1572-0.04030.00010.46770.01910.05830.41840.00430.38-9.6725-50.42910.8581
40.05350.2087-0.01871.04660.0725-0.0592-0.0621-0.07550.2919-0.102-0.31430.2422-0.1704-0.4155-0.00080.47030.01970.00370.445-0.03470.4745-12.009-41.935211.7998
50.5429-0.1152-0.2239-0.00830.11310.82850.02820.1747-0.0391-0.03750.3268-0.17440.0360.29480.00010.3174-0.01270.02340.3265-0.03070.3492-1.8627-42.8210.7685
6-0.1165-0.3311-0.06970.22120.48460.3450.07580.04960.0066-0.2973-0.0523-0.1546-0.2415-0.0649-00.5813-0.01530.09130.3975-0.03470.4319-4.2289-31.204915.7692
70.62140.1844-0.11161.46251.29510.91410.07630.04420.0319-0.0506-0.0258-0.0850.11920.133200.5153-0.0026-0.01670.4943-0.02360.5552-2.1053-14.096135.5177
80.18620.2116-0.16620.34680.29030.8403-0.1809-0.1523-0.178-0.22580.30120.16640.0242-0.185300.525-0.0244-0.01780.45480.01150.5429-5.135-11.43241.8237
90.1452-0.1890.27671.23151.45291.2240.02590.01520.0374-0.1968-0.04740.0806-0.1721-0.0345-00.5858-0.00430.04060.4424-0.06310.5438-4.6053-12.441836.0019
101.1574-0.28820.69160.0826-0.12950.4235-0.1630.1858-0.2452-0.95630.1782-0.7015-0.15730.0091-00.657-0.04260.06950.5149-0.04450.54631.2721-5.627729.9968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 177 )
7X-RAY DIFFRACTION7chain 'A' and (resid 178 through 220 )
8X-RAY DIFFRACTION8chain 'A' and (resid 221 through 237 )
9X-RAY DIFFRACTION9chain 'A' and (resid 238 through 279 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 14 )

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