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

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Basic information

Entry
Database: PDB / ID: 6gtz
TitleCrystal structure of a FimH*DsG complex from E.coli F18 with bound dimannoside Man(alpha1-3)Man in space group P21
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
FimH protein / FimG protein
Similarity search - Component
Biological speciesEscherichia coli F18+ (bacteria)
Escherichia coli 536 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.719 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_asym_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

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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)61,6526
Polymers60,9404
Non-polymers7132
Water14,556808
1
A: FimH protein
B: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8263
Polymers30,4702
Non-polymers3561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-6 kcal/mol
Surface area13460 Å2
MethodPISA
2
C: FimH protein
D: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8263
Polymers30,4702
Non-polymers3561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-7 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.637, 115.112, 63.158
Angle α, β, γ (deg.)90.00, 107.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 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: 1.0002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0002 Å / Relative weight: 1
ReflectionResolution: 1.719→42.553 Å / Num. obs: 123705 / % possible obs: 97 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rrim(I) all: 0.084 / Net I/σ(I): 9.2
Reflection shellResolution: 1.719→1.82 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6155 / CC1/2: 0.732 / Rrim(I) all: 0.732 / % possible all: 94.5

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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: 1.719→42.553 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2029 6199 5.01 %
Rwork0.1789 --
obs0.1802 123705 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.719→42.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 48 814 5140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044453
X-RAY DIFFRACTIONf_angle_d0.7256133
X-RAY DIFFRACTIONf_dihedral_angle_d11.2332589
X-RAY DIFFRACTIONf_chiral_restr0.052752
X-RAY DIFFRACTIONf_plane_restr0.004789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7192-1.73880.42871720.40883263X-RAY DIFFRACTION83
1.7388-1.75920.44742100.39113984X-RAY DIFFRACTION97
1.7592-1.78070.38792100.36313920X-RAY DIFFRACTION97
1.7807-1.80320.38372030.33893912X-RAY DIFFRACTION97
1.8032-1.82690.34992050.33053937X-RAY DIFFRACTION98
1.8269-1.8520.33462100.3193951X-RAY DIFFRACTION97
1.852-1.87840.32672080.28663877X-RAY DIFFRACTION96
1.8784-1.90650.29382010.26383772X-RAY DIFFRACTION94
1.9065-1.93630.29162080.24043958X-RAY DIFFRACTION98
1.9363-1.9680.25752080.21634002X-RAY DIFFRACTION99
1.968-2.00190.21872080.21073946X-RAY DIFFRACTION99
2.0019-2.03830.2322100.19974060X-RAY DIFFRACTION99
2.0383-2.07750.22962020.20963898X-RAY DIFFRACTION99
2.0775-2.11990.22412140.20264046X-RAY DIFFRACTION99
2.1199-2.1660.21532090.19883984X-RAY DIFFRACTION98
2.166-2.21640.21312110.17883948X-RAY DIFFRACTION99
2.2164-2.27190.23182090.17223961X-RAY DIFFRACTION99
2.2719-2.33330.19432080.17964007X-RAY DIFFRACTION98
2.3333-2.40190.23842080.1783937X-RAY DIFFRACTION99
2.4019-2.47940.21152160.17254007X-RAY DIFFRACTION98
2.4794-2.56810.19992090.17013948X-RAY DIFFRACTION98
2.5681-2.67090.22462020.17033840X-RAY DIFFRACTION96
2.6709-2.79240.18172070.16743974X-RAY DIFFRACTION97
2.7924-2.93960.20322090.17223955X-RAY DIFFRACTION99
2.9396-3.12370.17952100.16493936X-RAY DIFFRACTION98
3.1237-3.36480.16722090.14853921X-RAY DIFFRACTION97
3.3648-3.70320.17092060.14553925X-RAY DIFFRACTION96
3.7032-4.23870.14762020.13693841X-RAY DIFFRACTION96
4.2387-5.33860.1322040.1173821X-RAY DIFFRACTION95
5.3386-42.56580.1792110.16833975X-RAY DIFFRACTION98
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)
10.53530.295-0.041.50131.1830.9456-0.07350.12130.0149-0.5348-0.10220.1775-0.5455-0.30980.1230.47890.0893-0.08770.22-0.01960.24483.862-27.0628.4743
21.25750.194-0.31232.5947-0.05312.17840.123-0.03870.1172-0.4508-0.1210.0047-0.2587-0.05810.04220.32650.05730.01540.1596-0.01290.197610.4268-18.299521.0429
30.0582-0.39820.04661.85820.78531.57350.0132-0.03110.0548-0.6802-0.22090.2491-0.4794-0.32890.14470.34430.0898-0.0160.1992-0.02980.23155.0439-21.542516.2605
41.30590.1816-0.21470.08740.1660.72740.16230.0678-0.00490.83520.0664-0.397-0.4979-0.1363-0.08770.59740.06270.01750.17860.00430.182911.7257-16.228711.4731
510.9010.44160.70810.35250.50360.12-0.0158-0.28090.1047-0.018-0.16420.03320.1383-0.09170.2026-0.0093-0.02120.2359-0.01340.232214.7757-17.7211-11.7939
61.7780.84790.92321.01210.34390.7725-0.02580.0127-0.00350.0252-0.0190.0131-0.15240.06980.03710.2341-0.0271-0.01550.20690.00630.181210.4169-10.0783-12.3903
70.4438-0.12720.10381.52650.3220.8238-0.0093-0.03810.00470.1235-0.0181-0.02450.08340.01910.02080.1596-0.00560.02170.1589-0.00560.1848-9.8333-37.0583-25.6239
81.3357-0.19940.78111.5597-0.56111.01450.10060.0691-0.0978-0.1695-0.09220.18260.1749-0.078-0.0130.2175-0.00680.01560.1515-0.00460.191-13.3692-45.7546-34.9403
90.5744-0.2952-0.45111.5990.41470.38110.0316-0.1452-0.05650.3673-0.11570.20280.2739-0.21460.04960.261-0.03590.06190.2543-0.05210.2278-17.8478-32.5923-17.9953
100.9647-0.430.2522.0316-0.25630.85650.02670.0718-0.0703-0.2256-0.05610.19130.1621-0.03640.03130.2062-0.00660.01660.1809-0.00950.1879-12.3037-44.6201-33.3915
111.9675-1.01870.15090.9002-0.33150.99960.02870.02870.0391-0.62860.0199-0.51580.07160.09770.02870.15610.02010.04970.187-0.00980.161-6.1618-47.1085-30.9412
122.17850.5422-0.19293.88641.40712.4940.05750.09520.2181-0.18540.13450.1788-0.05440.166-0.07160.2806-0.013-0.00510.22050.0070.178514.2887-49.6276-23.7077
130.5033-0.3587-0.14610.50650.75841.2457-0.02360.02580.07330.03310.0479-0.0597-0.0381-0.04690.00010.36210.001-0.04610.2265-0.01880.22838.0587-50.5759-14.6614
141.32230.6185-0.02662.04340.97752.2302-0.1088-0.02620.11250.04850.0446-0.01380.0324-0.13180.09650.3040.0179-0.02890.1755-0.01880.20086.8293-52.0352-3.1288
150.649-0.05550.0560.50860.092.9249-0.11380.05710.00330.13950.0016-0.02250.4431-0.0574-0.00520.28270.0085-0.03260.1991-0.01710.15825.4115-57.1027-17.7356
160.2642-0.0885-0.19480.24430.52181.84480.0103-0.02490.03790.05170.0599-0.02070.08830.1677-0.06130.31640.0072-0.03630.2034-0.02090.183512.5358-51.3229-10.4059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 151 through 198 )
2X-RAY DIFFRACTION2chain 'C' and (resid 199 through 237 )
3X-RAY DIFFRACTION3chain 'C' and (resid 238 through 279 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 14 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 31 )
6X-RAY DIFFRACTION6chain 'A' and (resid 32 through 150 )
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 208 )
8X-RAY DIFFRACTION8chain 'A' and (resid 209 through 237 )
9X-RAY DIFFRACTION9chain 'A' and (resid 238 through 251 )
10X-RAY DIFFRACTION10chain 'A' and (resid 252 through 279 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 14 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 15 )
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 65 )
14X-RAY DIFFRACTION14chain 'C' and (resid 66 through 84 )
15X-RAY DIFFRACTION15chain 'C' and (resid 85 through 104 )
16X-RAY DIFFRACTION16chain 'C' and (resid 105 through 150 )

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