8BY3 | pdb_00008by3

FimH lectin domain in complex with oligomannose-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.238 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.209 (DCC) 

Starting Model: experimental
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Literature

Structural insights into a cooperative switch between one and two FimH bacterial adhesins binding pauci- and high-mannose type N-glycan receptors.

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.

(2023) J Biological Chem 299: 104627-104627

  • DOI: https://doi.org/10.1016/j.jbc.2023.104627
  • Primary Citation Related Structures: 
    7BHD, 8BXY, 8BY3

  • PubMed Abstract: 

    The FimH type-1 fimbrial adhesin allows pathogenic Escherichia coli to adhere to glycoproteins in the epithelial linings of human bladder and intestinal tract, by using multiple fimbriae simultaneously. Pauci- and high-mannose type N-glycans are natural FimH receptors on those glycoproteins. Oligomannose-3 and oligomannose-5 bind with the highest affinity to FimH by using the same Manα1,3Man branch. Oligomannose-6 is generated from oligomannose-5 in the next step of the biogenesis of high-mannose N-glycans, by the transfer of a mannose in α1,2-linkage onto this branch. Using serial crystallography and by measuring the kinetics of binding, we demonstrate that shielding the high-affinity epitope drives the binding of multiple FimH molecules. First, we profiled FimH glycan binding on a microarray containing paucimannosidic N-glycans and in a FimH LEctPROFILE assay. To make the transition to oligomannose-6, we measured the kinetics of FimH binding using paucimannosidic N-glycans, glycoproteins and all four α-dimannosides conjugated to bovine serum albumin. Equimolar mixed interfaces of the dimannosides present in oligomannose-6 and molecular dynamics simulations suggest a positive cooperativity in the bivalent binding of Manα1,3Manα1 and Manα1,6Manα1 dimannosides. The binding of core α1,6-fucosylated oligomannose-3 in cocrystals of FimH is monovalent but interestingly the GlcNAc1-Fuc moiety retains highly flexibility. In cocrystals with oligomannose-6, two FimH bacterial adhesins bind the Manα1,3Manα1 and Manα1,6Manα1 endings of the second trimannose core (A-4'-B). This cooperative switch towards bivalent binding appears sustainable beyond a molar excess of oligomannose-6. Our findings provide important novel structural insights for the design of multivalent FimH antagonists that bind with positive cooperativity.


  • Organizational Affiliation
    • Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576 CNRS and University of Lille, Villeneuve d'Ascq, France.

Macromolecule Content 

  • Total Structure Weight: 70.89 kDa 
  • Atom Count: 5,153 
  • Modeled Residue Count: 632 
  • Deposited Residue Count: 632 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type 1 fimbrin D-mannose specific adhesin
A, B, C, D
158Escherichia coli K-12Mutation(s): 0 
Gene Names: fimHb4320JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12))
Explore P08191 
Go to UniProtKB:  P08191
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08191
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
8N/A
Glycosylation Resources
GlyTouCan: G80966KZ
GlyCosmos: G80966KZ
GlyGen: G80966KZ

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.238 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.209 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.11α = 90
b = 153.11β = 90
c = 230.41γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union750280

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary