3F53

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2F-3'SiaLacNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii.

Garnett, J.A.Liu, Y.Leon, E.Allman, S.A.Friedrich, N.Saouros, S.Curry, S.Soldati-Favre, D.Davis, B.G.Feizi, T.Matthews, S.

(2009) Protein Sci 18: 1935-1947

  • DOI: 10.1002/pro.204
  • Primary Citation of Related Structures:  
    3F5E, 3F5A, 3F53

  • PubMed Abstract: 
  • The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands ...

    The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands. Here, we investigate by further microarray analyses in a dose-response format the differential binding of TgMIC1 to 2-3- and 2-6-linked sialyl carbohydrates. Interestingly, two novel synthetic fluorinated analogs of 3'SiaLacNAc(1-4) and 3'SiaLacNAc(1-3) were identified as highly potent ligands. To understand the structural basis of the carbohydrate binding specificity of TgMIC1, we have determined the crystal structures of TgMIC1 micronemal adhesive repeat (MAR)-region (TgMIC1-MARR) in complex with five sialyl-N-acetyllactosamine analogs. These crystal structures have revealed a specific, water-mediated hydrogen bond network that accounts for the preferential binding of TgMIC1-MARR to arrayed 2-3-linked sialyl oligosaccharides and the high potency of the fluorinated analogs. Furthermore, we provide strong evidence for the first observation of a C--F...H--O hydrogen bond within a lectin-carbohydrate complex. Finally, detailed comparison with other oligosaccharide-protein complexes in the Protein Data Bank (PDB) reveals a new family of sialic-acid binding sites from lectins in parasites, bacteria, and viruses.


    Related Citations: 
    • Atomic resolution insight into host cell recognition by Toxoplasma gondii.
      Blumenschein, T.M., Friedrich, N., Childs, R.A., Saouros, S., Carpenter, E.P., Campanero-Rhodes, M.A., Simpson, P., Chai, W., Koutroukides, T., Blackman, M.J., Feizi, T., Soldati-Favre, D., Matthews, S.
      (2007) EMBO J 26: 2808

    Organizational Affiliation

    Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW72AZ, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Micronemal protein 1A246Toxoplasma gondii RHMutation(s): 0 
Gene Names: MIC1
UniProt
Find proteins for O00834 (Toxoplasma gondii)
Explore O00834 
Go to UniProtKB:  O00834
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranoseB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G93558HL
GlyCosmos:  G93558HL
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.361α = 90
b = 66.361β = 90
c = 172.371γ = 90
Software Package:
Software NamePurpose
ADSC Quantumdata collection
PHASERphasing
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2008-11-03 
  • Released Date: 2009-07-28 
  • Deposition Author(s): Garnett, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary