3FFO | pdb_00003ffo

F17b-G lectin domain with bound GlcNAc(beta1-2)man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.271 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3FFO

This is version 2.2 of the entry. See complete history

Literature

Structural Sampling of Glycan Interaction Profiles Reveals Mucosal Receptors for Fimbrial Adhesins of Enterotoxigenic Escherichia coli.

Lonardi, E.Moonens, K.Buts, L.de Boer, A.R.Olsson, J.D.M.Weiss, M.S.Fabre, E.Guerardel, Y.Deelder, A.M.Oscarson, S.Wuhrer, M.Bouckaert, J.

(2013) Biology (Basel) 2: 894-917

  • DOI: https://doi.org/10.3390/biology2030894
  • Primary Citation Related Structures: 
    3F64, 3F6J, 3FFO, 4BWO, 4K0O

  • PubMed Abstract: 

    Fimbriae are long, proteinaceous adhesion organelles expressed on the bacterial envelope, evolutionarily adapted by Escherichia coli strains for the colonization of epithelial linings. Using glycan arrays of the Consortium for Functional Glycomics (CFG), the lectin domains were screened of the fimbrial adhesins F17G and FedF from enterotoxigenic E. coli (ETEC) and of the FimH adhesin from uropathogenic E. coli. This has led to the discovery of a more specific receptor for F17G, GlcNAcb1,3Gal. No significant differences emerged from the glycan binding profiles of the F17G lectin domains from five different E. coli strains. However, strain-dependent amino acid variations, predominantly towards the positively charged arginine, were indicated by sulfate binding in FedF and F17G crystal structures. For FedF, no significant binders could be observed on the CFG glycan array. Hence, a shotgun array was generated from microvilli scrapings of the distal jejunum of a 3-week old piglet about to be weaned. On this array, the blood group A type 1 hexasaccharide emerged as a receptor for the FedF lectin domain and remarkably also for F18-fimbriated E. coli. F17G was found to selectively recognize glycan species with a terminal GlcNAc, typifying intestinal mucins. In conclusion, F17G and FedF recognize long glycan sequences that could only be identified using the shotgun approach. Interestingly, ETEC strains display a large capacity to adapt their fimbrial adhesins to ecological niches via charge-driven interactions, congruent with binding to thick mucosal surfaces displaying an acidic gradient along the intestinal tract.


  • Organizational Affiliation
    • Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, RC Leiden 2300, The Netherlands. e.lonardi@lumc.nl.

Macromolecule Content 

  • Total Structure Weight: 19.65 kDa 
  • Atom Count: 1,408 
  • Modeled Residue Count: 176 
  • Deposited Residue Count: 176 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adhesin176Escherichia coliMutation(s): 0 
Gene Names: F17b-G
UniProt
Find proteins for Q47200 (Escherichia coli)
Explore Q47200 
Go to UniProtKB:  Q47200
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47200
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G43534QA
GlyCosmos: G43534QA
GlyGen: G43534QA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.271 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.389α = 90
b = 87.389β = 90
c = 56.809γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2013-08-28
    Changes: Database references, Non-polymer description
  • Version 1.3: 2014-12-17
    Changes: Atomic model, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary