8RCY | pdb_00008rcy

L-SIGN CRD in complex with Man84.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.217 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Literature

Unprecedented selectivity for homologous lectin targets: differential targeting of the viral receptors L-SIGN and DC-SIGN.

Delaunay, C.Pollastri, S.Thepaut, M.Cavazzoli, G.Belvisi, L.Bouchikri, C.Labiod, N.Lasala, F.Gimeno, A.Franconetti, A.Jimenez-Barbero, J.Arda, A.Delgado, R.Bernardi, A.Fieschi, F.

(2024) Chem Sci 15: 15352-15366

  • DOI: https://doi.org/10.1039/d4sc02980a
  • Primary Citation of Related Structures:  
    8RCY

  • PubMed Abstract: 

    DC-SIGN (CD209) and L-SIGN (CD209L) are two C-type lectin receptors (CLRs) that facilitate SARS-CoV-2 infections as viral co-receptors. SARS-CoV-2 manipulates both DC-SIGN and L-SIGN for enhanced infection, leading to interest in developing receptor antagonists. Despite their structural similarity (82% sequence identity), they function differently. DC-SIGN, found in dendritic cells, shapes the immune response by recognizing pathogen-associated carbohydrate patterns. In contrast, L-SIGN, expressed in airway epithelial endothelial cells, is not directly involved in immunity. COVID-19's primary threat is the hyperactivation of the immune system, potentially reinforced if DC-SIGN engages with exogenous ligands. Therefore, L-SIGN, co-localized with ACE2-expressing cells in the respiratory tract, is a more suitable target for anti-adhesion therapy. However, designing a selective ligand for L-SIGN is challenging due to the high sequence identity of the Carbohydrate Recognition Domains (CRDs) of the two lectins. We here present Man84, a mannose ring modified with a methylene guanidine triazole at position 2. It binds L-SIGN with a K D of 12.7μM ± 1 μM (ITC) and is the first known L-SIGN selective ligand, showing 50-fold selectivity over DC-SIGN (SPR). The X-ray structure of the L-SIGN CRD/Man84 complex reveals the guanidinium group's role in achieving steric and electrostatic complementarity with L-SIGN. This allows us to trace the source of selectivity to a single amino acid difference between the two CRDs. NMR analysis confirms the binding mode in solution, highlighting Man84's conformational selection upon complex formation. Dimeric versions of Man84 achieve additional selectivity and avidity in the low nanomolar range. These compounds selectively inhibit L-SIGN dependent trans-infection by SARS-CoV-2 and Ebola virus. Man84 and its dimeric constructs display the best affinity and avidity reported to date for low-valency glycomimetics targeting CLRs. They are promising tools for competing with SARS-CoV-2 anchoring in the respiratory tract and have potential for other medical applications.


  • Organizational Affiliation
    • Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale Grenoble France franck.fieschi@ibs.fr.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member M137Homo sapiensMutation(s): 0 
Gene Names: CLEC4MCD209LCD209L1CD299
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X3 (Homo sapiens)
Explore Q9H2X3 
Go to UniProtKB:  Q9H2X3
PHAROS:  Q9H2X3
GTEx:  ENSG00000104938 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2X3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.217 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.43α = 90
b = 48.89β = 103.53
c = 35.67γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceCBH-EUR-GS (ANR-17- EURE0003)
Ministero dell Universita e della RicercaItaly--
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)Italy--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release