5G6U | pdb_00005g6u

Crystal structure of langerin carbohydrate recognition domain with GlcNS6S

• PDB DOI: https://doi.org/10.2210/pdb5G6U/pdb

• Classification: CARBOHYDRATE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-21 Released: 2018-02-21 
• Deposition Author(s): Porkolab, V., Chabrol, E., Varga, N., Ordanini, S., Sutkeviciute, I., Thepaut, M., Bernardi, A., Fieschi, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.180 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Rational-Differential Design of Highly Specific Glycomimetic Ligands: Targeting DC-SIGN and Excluding Langerin Recognition.

Porkolab, V., Chabrol, E., Varga, N., Ordanini, S., Sutkeviciu Te, I., Thepaut, M., Garcia-Jimenez, M.J., Girard, E., Nieto, P.M., Bernardi, A., Fieschi, F.

(2018) ACS Chem Biol 13: 600-608

• PubMed: 29272097 
• DOI: https://doi.org/10.1021/acschembio.7b00958
• Primary Citation Related Structures: 
  5G6U


• PubMed Abstract: 
  

  At the surface of dendritic cells, C-type lectin receptors (CLRs) allow the recognition of carbohydrate-based PAMPS or DAMPS (pathogen- or danger-associated molecular patterns, respectively) and promote immune response regulation. However, some CLRs are hijacked by viral and bacterial pathogens. Thus, the design of ligands able to target specifically one CLR, to either modulate an immune response or to inhibit a given infection mechanism, has great potential value in therapeutic design. A case study is the selective blocking of DC-SIGN, involved notably in HIV trans-infection of T lymphocytes, without interfering with langerin-mediated HIV clearance. This is a challenging task due to their overlapping carbohydrate specificity. Toward the rational design of DC-SIGN selective ligands, we performed a comparative affinity study between DC-SIGN and langerin with natural ligands. We found that GlcNAc is recognized by both CLRs; however, selective sulfation are shown to increase the selectivity in favor of langerin. With the combination of site-directed mutagenesis and X-ray structural analysis of the langerin/GlcNS6S complex, we highlighted that 6-sulfation of the carbohydrate ligand induced langerin specificity. Additionally, the K313 residue from langerin was identified as a critical feature of its binding site. Using a rational and a differential approach in the study of CLR binding sites, we designed, synthesized, and characterized a new glycomimetic, which is highly specific for DC-SIGN vs langerin. STD NMR, SPR, and ITC characterizations show that compound 7 conserved the overall binding mode of the natural disaccharide while possessing an improved affinity and a strict specificity for DC-SIGN.

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Organizational Affiliation: 
• Univ. Grenoble Alpes , CNRS, CEA, Institut de Biologie Structurale , F-38044 Grenoble , France.
Università degli Studi di Milano (UniMI) , Dip. Chimica, via Golgi 19 , 20133 , Milano , Italy.
Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja , CSIC and Universidad de Sevilla , Américo Vespucio, 49 , 41092 Sevilla , Spain.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 121.33 kDa 
• Atom Count: 4,932 
• Modeled Residue Count: 514 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LANGERIN	A, B, C, D	261	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ71 (Homo sapiens) Explore Q9UJ71  Go to UniProtKB:  Q9UJ71
PHAROS:  Q9UJ71 GTEx:  ENSG00000116031

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SGN	CA [auth D], F [auth A], L [auth B], U [auth C]	2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose C6 H13 N O11 S2 DQTRACMFIGDHSN-UKFBFLRUSA-N
TRP	BA [auth D], E [auth A], K [auth B]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
EU	G [auth A], J [auth A], M [auth B], T [auth B], W [auth C], X [auth C]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N
CA	DA [auth D], H [auth A], N [auth B], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	AA [auth C], EA [auth D], FA [auth D], GA [auth D], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.180 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.483	α = 90
b = 79.483	β = 90
c = 90.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Porkolab, V., Chabrol, E., Varga, N., Ordanini, S., Sutkeviciute, I., Thepaut, M., Bernardi, A., Fieschi, F.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2018-02-28
  Changes: Derived calculations
• Version 1.2: 2018-03-28
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary