2XR5

Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a Glycomimetic Ligand in the Carbohydrate Recognition Domain of C-Type Lectin Dc-Sign. Structural Requirements for Selectivity and Ligand Design.

Thepaut, M.Guzzi, C.Sutkeviciute, I.Sattin, S.Ribeiro-Viana, R.Varga, N.Chabrol, E.Rojo, J.Bernardi, A.Angulo, J.Nieto, P.M.Fieschi, F.

(2013) J.Am.Chem.Soc. 135: 2518

  • DOI: 10.1021/ja3053305

  • PubMed Abstract: 
  • In genital mucosa, different fates are described for HIV according to the subtype of dendritic cells (DCs) involved in its recognition. This notably depends on the C-type lectin receptor, langerin or DC-SIGN, involved in gp120 interaction. Langerin b ...

    In genital mucosa, different fates are described for HIV according to the subtype of dendritic cells (DCs) involved in its recognition. This notably depends on the C-type lectin receptor, langerin or DC-SIGN, involved in gp120 interaction. Langerin blocks HIV transmission by its internalization in specific organelles of Langerhans cells. On the contrary, DC-SIGN enhances HIV trans-infection of T lymphocytes. Thus, approaches aiming to inhibit DC-SIGN, without blocking langerin, represent attractive anti-HIV strategies. We previously demonstrated that dendrons bearing multiple copies of glycomimetic compounds were able to block DC-SIGN-dependent HIV infection in cervical explant models. Optimization of such ligand requires detailed characterization of its binding mode. In the present work, we determined the first high-resolution structure of a glycomimetic/DC-SIGN complex by X-ray crystallography. This glycomimetic, pseudo-1,2-mannobioside, shares shape and conformational properties with Man╬▒1-2Man, its natural counterpart. However, it uses the binding epitope previously described for Lewis X, a ligand specific for DC-SIGN among the C-type lectin family. Thus, selectivity gain for DC-SIGN versus langerin is observed with pseudo-1,2-mannobioside as shown by surface plasmon resonance analysis. In parallel, ligand binding was also analyzed by TR-NOESY and STD NMR experiments, combined with the CORCEMA-ST protocol. These studies demonstrate that the complex, defined by X-ray crystallography, represents the unique binding mode of this ligand as opposed to the several binding orientations described for the natural ligand. This exclusive binding mode and its selective interaction properties position this glycomimetic as a good lead compound for rational improvement based on a structurally driven approach.


    Organizational Affiliation

    Institut de Biologie Structurale, Universit├ę Grenoble I, 41 rue Jules Horowitz, Grenoble, F-38027, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD209 ANTIGEN
A
166Homo sapiensMutation(s): 0 
Gene Names: CD209 (CLEC4L)
Find proteins for Q9NNX6 (Homo sapiens)
Go to Gene View: CD209
Go to UniProtKB:  Q9NNX6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
07B
Query on 07B

Download SDF File 
Download CCD File 
A
dimethyl (1S,2S,4S,5S)-4,5-dihydroxycyclohexane-1,2-dicarboxylate
C10 H16 O6
ICVNZKRWDVXSLF-XAMCCFCMSA-N
 Ligand Interaction
ETA
Query on ETA

Download SDF File 
Download CCD File 
A
ETHANOLAMINE
C2 H7 N O
HZAXFHJVJLSVMW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.450α = 90.00
b = 71.450β = 90.00
c = 52.670γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references