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- PDB-7bhd: FimH in complex with alpha1,6 core-fucosylated oligomannose-3, cr... -

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Basic information

Entry
Database: PDB / ID: 7bhd
TitleFimH in complex with alpha1,6 core-fucosylated oligomannose-3, crystallized in the trigonal space group
ComponentsType 1 fimbrin D-mannose specific adhesin
KeywordsCELL ADHESION / adhesin / FimH / core fucose
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBridot, C. / Bouckaert, J. / Krammer, E.-M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission750280European Union
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: Structural insights into a cooperative switch between one and two FimH bacterial adhesins binding pauci- and high-mannose type N-glycan receptors.
Authors: Krammer, E.M. / Bridot, C. / Serna, S. / Echeverria, B. / Semwal, S. / Roubinet, B. / van Noort, K. / Wilbers, R.H.P. / Bourenkov, G. / de Ruyck, J. / Landemarre, L. / Reichardt, N. / Bouckaert, J.
#1: Journal: PLoS One / Year: 2008
Title: Intervening with urinary tract infections using anti-adhesives based on the crystal structure of the FimH-oligomannose-3 complex.
Authors: Wellens, A. / Garofalo, C. / Nguyen, H. / Van Gerven, N. / Slattegard, R. / Hernalsteens, J.P. / Wyns, L. / Oscarson, S. / De Greve, H. / Hultgren, S. / Bouckaert, J.
#2: Journal: Molecules / Year: 2017
Title: Sites for Dynamic Protein-Carbohydrate Interactions of O- and C-Linked Mannosides on the E. coli FimH Adhesin.
Authors: Touaibia, M. / Krammer, E.M. / Shiao, T.C. / Yamakawa, N. / Wang, Q. / Glinschert, A. / Papadopoulos, A. / Mousavifar, L. / Maes, E. / Oscarson, S. / Vergoten, G. / Lensink, M.F. / Roy, R. / Bouckaert, J.
#3: Journal: Molecules / Year: 2018
Title: A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin.
Authors: Dumych, T. / Bridot, C. / Gouin, S.G. / Lensink, M.F. / Paryzhak, S. / Szunerits, S. / Blossey, R. / Bilyy, R. / Bouckaert, J. / Krammer, E.M.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type 1 fimbrin D-mannose specific adhesin
B: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,44910
Polymers33,8342
Non-polymers2,6168
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-17 kcal/mol
Surface area14530 Å2
Unit cell
Length a, b, c (Å)91.210, 91.210, 79.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-354-

HOH

21B-405-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 43 or resid 45 through 158 or resid 200 through 303 or resid 306))
d_2ens_1(chain "B" and (resid 1 through 43 or resid 45 through 158 or resid 200 through 303 or resid 306))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PHEPHEA1 - 43
d_12ens_1HISTHRA45 - 158
d_13ens_1NINIE3
d_14ens_1SO4SO4F - G4
d_15ens_1MANMANC2
d_16ens_1BMABMAC2
d_17ens_1NAGNAGF2
d_18ens_1MANMANI2
d_21ens_1PHEPHEB1 - 43
d_22ens_1HISTHRB45 - 158
d_23ens_1NINIH3
d_24ens_1SO4SO4I - J4
d_25ens_1MANMAND2
d_26ens_1BMABMAD2
d_27ens_1NAGNAGD2
d_28ens_1MANMAND2

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Components

#1: Protein Type 1 fimbrin D-mannose specific adhesin / Protein FimH


Mass: 16916.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.65 Å3/Da / Density % sol: 53.66 % / Description: diamond-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1,1M Lithium sulfate, 0,1M Tris-HCl pH=9, 0,01M Nickel Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→78.99 Å / Num. obs: 75457 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 19.15 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.077 / Net I/σ(I): 17.01
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 15.57 % / Rmerge(I) obs: 4.192 / Mean I/σ(I) obs: 0.42 / Num. unique obs: 11867 / CC1/2: 0.184 / Rrim(I) all: 4.331 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.17.1_3660model building
autoPROCdata processing
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VCO

2vco


Resolution: 1.4→78.99 Å / SU ML: 0.2181 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.0644
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 1853 2.65 %Random selection
Rwork0.1708 68099 --
obs0.1716 69952 92.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.25 Å2
Refinement stepCycle: LAST / Resolution: 1.4→78.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 166 483 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02412651
X-RAY DIFFRACTIONf_angle_d2.04543651
X-RAY DIFFRACTIONf_chiral_restr0.1183455
X-RAY DIFFRACTIONf_plane_restr0.0133447
X-RAY DIFFRACTIONf_dihedral_angle_d13.8849465
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.29284061315 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.46891010.41753853X-RAY DIFFRACTION68.56
1.44-1.480.40251250.34594346X-RAY DIFFRACTION77.27
1.48-1.530.35821290.28784611X-RAY DIFFRACTION82.49
1.53-1.580.24381320.23534939X-RAY DIFFRACTION87.45
1.58-1.640.22181420.20315158X-RAY DIFFRACTION92.29
1.64-1.720.26741510.20215394X-RAY DIFFRACTION95.44
1.72-1.810.2331470.20125515X-RAY DIFFRACTION97.32
1.81-1.920.24131500.20765585X-RAY DIFFRACTION99.17
1.92-2.070.22041540.16495646X-RAY DIFFRACTION99.85
2.07-2.280.1811540.17425687X-RAY DIFFRACTION99.97
2.28-2.610.19281510.17965707X-RAY DIFFRACTION99.98
2.61-3.290.18221520.16825744X-RAY DIFFRACTION100
3.29-78.990.17861650.14335914X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -33.6803109658 Å / Origin y: -22.7769156472 Å / Origin z: -5.94853275097 Å
111213212223313233
T0.194745399306 Å2-0.0111775152924 Å20.000845301827032 Å2-0.126268421352 Å20.0137042300851 Å2--0.192263628885 Å2
L1.12559352378 °2-0.300946004283 °2-0.32666382934 °2-0.463718740923 °20.35729590043 °2--1.70319753775 °2
S0.0647332222147 Å °0.0547596830076 Å °0.161395416637 Å °-0.019972457843 Å °-0.0320250813621 Å °-0.099048317729 Å °-0.0092385554159 Å °0.0096918751821 Å °-0.0257128734542 Å °
Refinement TLS groupSelection details: all

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