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- PDB-6gtw: Crystal structure of the FimH lectin domain from E.coli F18 in co... -

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Basic information

Entry
Database: PDB / ID: 6gtw
TitleCrystal structure of the FimH lectin domain from E.coli F18 in complex with trimannose
ComponentsFimH 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
Biological speciesEscherichia coli F18+ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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: FimH protein
C: FimH protein
D: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9129
Polymers67,7834
Non-polymers1,1295
Water6,864381
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A: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9862
Polymers16,9461
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4903
Polymers16,9461
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FimH protein


Theoretical massNumber of molelcules
Total (without water)16,9461
Polymers16,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4903
Polymers16,9461
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.180, 175.180, 124.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
FimH protein


Mass: 16945.826 Da / Num. of mol.: 4
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: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 0.1 M Hepes-NaOH pH 7.0, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.36246 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36246 Å / Relative weight: 1
ReflectionResolution: 2.5→64.801 Å / Num. obs: 49294 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.994 / Rrim(I) all: 0.248 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7890 / CC1/2: 0.678 / Rrim(I) all: 2.033 / % possible all: 99.8

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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: 4XOC

4xoc


Resolution: 2.5→64.801 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2495 5.06 %
Rwork0.1917 --
obs0.1929 49294 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→64.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 71 381 5234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054978
X-RAY DIFFRACTIONf_angle_d0.96852
X-RAY DIFFRACTIONf_dihedral_angle_d10.9592914
X-RAY DIFFRACTIONf_chiral_restr0.053814
X-RAY DIFFRACTIONf_plane_restr0.005876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54810.36421590.34972562X-RAY DIFFRACTION100
2.5481-2.60010.35711480.33542586X-RAY DIFFRACTION100
2.6001-2.65670.35471480.332605X-RAY DIFFRACTION100
2.6567-2.71850.35071260.30632587X-RAY DIFFRACTION100
2.7185-2.78640.30441270.29222623X-RAY DIFFRACTION100
2.7864-2.86180.3171340.30422608X-RAY DIFFRACTION100
2.8618-2.9460.311510.31062585X-RAY DIFFRACTION100
2.946-3.04110.30431470.26262612X-RAY DIFFRACTION100
3.0411-3.14980.24661370.22832559X-RAY DIFFRACTION100
3.1498-3.27590.24151320.20712621X-RAY DIFFRACTION100
3.2759-3.4250.2221360.19562631X-RAY DIFFRACTION100
3.425-3.60550.19951250.18242582X-RAY DIFFRACTION100
3.6055-3.83140.21581290.17032627X-RAY DIFFRACTION100
3.8314-4.12720.15231260.13942628X-RAY DIFFRACTION100
4.1272-4.54240.14331440.12132592X-RAY DIFFRACTION100
4.5424-5.19950.12821320.11862608X-RAY DIFFRACTION100
5.1995-6.54980.17551520.1462592X-RAY DIFFRACTION100
6.5498-64.82290.21471420.18542591X-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)
10.06330.07010.05860.1820.22230.18570.37950.1181-0.1951-0.1202-0.01770.5111-0.02610.32110.00030.42010.0423-0.04190.43110.02350.546897.4777163.4059-1.8063
20.7845-0.3254-0.17140.6031-0.36470.69570.0146-0.0584-0.2425-0.02560.04940.09360.040.00730.00010.4311-0.0143-0.04070.37740.01750.5031106.4837157.94776.2704
30.5619-0.2876-0.23340.4842-0.45960.54910.0580.0727-0.4096-0.02580.10780.13240.17970.2735-00.4290.0272-0.03520.3545-0.02650.4226111.3303156.56691.6443
4-0.0078-0.0249-0.01090.16080.1320.14910.2215-0.2582-0.01970.4760.2554-0.11740.0711-0.2266-00.56440.0124-0.07160.4496-0.00990.5206105.7387157.559625.9368
51.0402-0.35750.35110.35280.2430.3854-0.03050.063-0.1975-0.0288-0.0386-0.0123-0.15130.038-0.00010.37210.0189-0.00940.3545-0.00230.4189105.7665163.73915.1709
60.07960.09260.0630.09640.07690.0573-0.0296-0.03240.02140.28880.12650.3756-0.27680.26790.00020.4780.0920.02590.4761-0.02330.463294.2875180.056423.0291
70.24860.17390.35560.08950.18790.4817-0.1383-0.1375-0.41510.4985-0.0850.0783-0.2141-0.049400.4709-0.0020.04810.5180.05750.4212112.7321173.85329.7645
80.14010.15290.07580.1144-0.02790.016-0.33340.082-0.31240.13560.17210.0803-0.1423-0.0190.00020.449-0.00130.0350.46450.03960.4632104.936172.267722.2484
90.03950.03390.00450.0432-0.0350.04350.30430.07210.162-0.22220.1220.00730.44250.0029-0.00020.42690.0134-0.01320.46670.07340.45786.9179177.99527.9202
100.0428-0.02050.07750.0083-0.06750.0408-0.27630.47570.42990.10410.14830.1092-0.0760.5479-0.00090.48020.0295-0.00980.4577-0.00960.4095106.404183.703915.4576
110.075-0.1667-0.03460.26140.14450.09680.0670.01160.2656-0.01530.0327-0.1594-0.0849-0.07680.00010.3662-0.0057-0.01120.4849-0.00130.3711117.8469178.184821.9504
120.2467-0.125-0.11220.07210.14510.33990.02970.0708-0.3176-0.0776-0.0056-0.0138-0.2906-0.007900.3966-0.0079-0.0010.44570.00670.4291109.5059178.829611.0513
130.149-0.0397-0.14680.0806-0.13080.21330.0115-0.3035-0.08080.0426-0.02210.04990.0098-0.2297-0.00020.40750.00720.03880.42960.01950.4429103.8236172.869417.6078
140.01640.0415-0.0380.1715-0.07490.0275-0.1425-0.11690.68380.57490.239-0.32980.1648-0.16520.00020.48090.0255-0.05310.571-0.03370.409121.8792177.530334.555
150.2661-0.1826-0.15680.00950.08940.0853-0.25280.1120.48090.1956-0.08710.3101-0.1308-0.147-0.00130.43060.0279-0.00430.4197-0.00660.3677104.0127184.112917.7569
160.22570.32330.0910.35210.1160.00280.0086-0.13240.18280.0022-0.07680.0242-0.0661-0.073500.42280.02620.02360.5201-0.03270.4248106.0578181.354322.9393
170.05840.0302-0.11320.12930.01190.258-0.1677-0.2134-0.15150.0161-0.05210.24730.01070.3964-0.00530.44110.08030.01830.3555-0.02520.497678.2694182.4611-3.4024
180.5641-0.1711-0.76480.48650.41070.8069-0.07490.03110.0179-0.13340.03350.15570.0993-0.2614-00.4094-0.0405-0.08690.3550.02670.432369.1323187.6228-16.2118
19-0.06190.09090.0190.45750.10370.0349-0.06360.01630.11060.1042-0.04420.0061-0.009-0.2425-00.3695-0.0094-0.00890.38980.01210.424677.867193.10060.4808
200.18920.07620.01280.0805-0.00190.0142-0.1940.31870.1132-0.26190.14390.22810.0452-0.02200.5175-0.0146-0.10160.47220.06110.477672.0384197.0898-20.6758
210.2850.09890.34830.07630.00920.2955-0.04670.0420.09680.0573-0.18440.1703-0.4065-0.28040.00010.49450.0695-0.01130.44150.03510.460472.9166200.7024-7.1802
220.0184-0.2328-0.06160.23280.13410.0586-0.0673-0.08190.03740.3044-0.1650.3008-0.30780.00540.00020.43230.0001-0.00820.427-0.00410.440369.0624191.1292-6.6757
230.1366-0.0354-0.111-0.00570.02850.10710.07390.3495-0.0808-0.33650.1934-0.50920.42640.0185-0.00030.5222-0.0469-0.02870.55210.03070.387472.2525190.3273-31.1724
240.1233-0.0407-0.23480.385-0.28090.4461-0.0190.05020.0950.0082-0.06490.04490.06110.1051-00.40860.0143-0.01990.3873-0.00270.433878.3959190.7327-10.4059
250.00930.01-0.05460.1129-0.0180.1629-0.08010.6923-0.7427-0.1338-0.11830.08570.00620.50070.00040.54790.1113-0.00560.4792-0.07250.444495.0233179.443-28.2087
260.11210.1661-0.23420.1429-0.25840.4707-0.04080.0894-0.1408-0.17980.05110.59160.14410.006300.550.0272-0.08510.4501-0.06340.474588.5569197.9117-35.0469
270.12850.15530.06970.1339-0.01790.04260.16730.2122-0.07750.0435-0.2585-0.01230.12850.171600.49740.0027-0.03680.48280.03520.410687.01190.0831-27.5198
280.0157-0.0280.02080.0263-0.02530.03510.161-0.1622-0.00250.1945-0.03260.411-0.1404-0.00580.00020.42470.0384-0.03680.3754-0.01380.442492.8833172.2147-13.0928
290.14660.05870.14390.04720.0020.062-0.00930.263-0.03840.2791-0.0089-0.211-0.1823-0.1808-00.44770.0628-0.00330.4424-0.01790.442998.4105191.7196-20.624
300.19120.06510.09130.00670.0340.1102-0.04570.00620.3427-0.39750.32130.21130.5322-0.0720.00020.4714-0.01-0.00540.41570.01710.437592.7427202.9932-27.2564
310.10870.17140.21530.19480.25250.3561-0.01470.00650.06230.2722-0.04080.3426-0.03120.26640.00010.4498-0.0233-0.0220.42070.00610.439593.4325194.7809-16.2775
320.00230.0416-0.01260.02390.07770.2838-0.0394-0.0052-0.05330.15010.14720.00820.094-0.09760.00010.4782-0.0364-0.06440.3992-0.01240.413787.5958189.0101-22.8472
330.20850.1606-0.14730.0992-0.07610.08720.04670.39620.1062-0.1725-0.29290.098-0.0418-0.18510.00010.47490.0013-0.01080.47960.04270.394992.2048207.0552-39.8258
34-0.0463-0.1194-0.02490.28740.13060.043-0.082-0.1019-0.24080.1882-0.1951-0.333-0.07760.0308-0.00110.43840.03280.00840.39680.00890.388498.8306189.3374-22.954
350.3020.59830.080.5973-0.1960.22040.04430.0933-0.0481-0.1501-0.1161-0.14040.09210.2525-00.49020.03440.03210.424-0.03810.379596.1065191.3226-28.1589
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 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 111 )
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 158 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 15 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 32 )
8X-RAY DIFFRACTION8chain 'B' and (resid 33 through 45 )
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 64 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 95 )
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 111 )
14X-RAY DIFFRACTION14chain 'B' and (resid 112 through 124 )
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 135 )
16X-RAY DIFFRACTION16chain 'B' and (resid 136 through 159 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 15 )
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 45 )
19X-RAY DIFFRACTION19chain 'C' and (resid 46 through 64 )
20X-RAY DIFFRACTION20chain 'C' and (resid 65 through 77 )
21X-RAY DIFFRACTION21chain 'C' and (resid 78 through 95 )
22X-RAY DIFFRACTION22chain 'C' and (resid 96 through 111 )
23X-RAY DIFFRACTION23chain 'C' and (resid 112 through 124 )
24X-RAY DIFFRACTION24chain 'C' and (resid 125 through 158 )
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 15 )
26X-RAY DIFFRACTION26chain 'D' and (resid 16 through 32 )
27X-RAY DIFFRACTION27chain 'D' and (resid 33 through 45 )
28X-RAY DIFFRACTION28chain 'D' and (resid 46 through 53 )
29X-RAY DIFFRACTION29chain 'D' and (resid 54 through 64 )
30X-RAY DIFFRACTION30chain 'D' and (resid 65 through 77 )
31X-RAY DIFFRACTION31chain 'D' and (resid 78 through 95 )
32X-RAY DIFFRACTION32chain 'D' and (resid 96 through 111 )
33X-RAY DIFFRACTION33chain 'D' and (resid 112 through 124 )
34X-RAY DIFFRACTION34chain 'D' and (resid 125 through 135 )
35X-RAY DIFFRACTION35chain 'D' and (resid 136 through 159 )

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