3C22

Crystal structure of the carbohydrate recognition domain of human Langerin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural studies of langerin and Birbeck granule: a macromolecular organization model

Thepaut, M.Valladeau, J.Nurisso, A.Kahn, R.Arnou, B.Vives, C.Saeland, S.Ebel, C.Monnier, C.Dezutter-Dambuyant, C.Imberty, A.Fieschi, F.

(2009) Biochemistry 48: 2684-2698

  • DOI: 10.1021/bi802151w

  • PubMed Abstract: 
  • Dendritic cells, a sentinel immunity cell lineage, include different cell subsets that express various C-type lectins. For example, epidermal Langerhans cells express langerin, and some dermal dendritic cells express DC-SIGN. Langerin is a crucial co ...

    Dendritic cells, a sentinel immunity cell lineage, include different cell subsets that express various C-type lectins. For example, epidermal Langerhans cells express langerin, and some dermal dendritic cells express DC-SIGN. Langerin is a crucial component of Birbeck granules, the Langerhans cell hallmark organelle, and may have a preventive role toward HIV, by its internalization into Birbeck granules. Since langerin carbohydrate recognition domain (CRD) is crucial for HIV interaction and Birbeck granule formation, we produced the CRD of human langerin and solved its structure at 1.5 A resolution. On this basis gp120 high-mannose oligosaccharide binding has been evaluated by molecular modeling. Hydrodynamic studies reveal a very elongated shape of recombinant langerin extracellular domain (ECD). A molecular model of the langerin ECD, integrating the CRD structure, has been generated and validated by comparison with hydrodynamic parameters. In parallel, Langerhans cells were isolated from human skin. From their analysis by electron microscopy and the langerin ECD model, an ultrastructural organization is proposed for Birbeck granules. To delineate the role of the different langerin domains in Birbeck granule formation, we generated truncated and mutated langerin constructs. After transfection into a fibroblastic cell line, we highlighted, in accordance with our model, the role of the CRD in the membrane zipping occurring in BG formation as well as some contribution of the cytoplasmic domain. Finally, we have shown that langerin ECD triggering with a specific mAb promotes global rearrangements of LC morphology. Our results open the way to the definition of a new membrane deformation mechanism.


    Related Citations: 
    • Overproduction, purification and preliminary crystallographic analysis of the carbohydrate-recognition domain of human langerin
      Thepaut, M.,Vives, C.,Pompidor, G.,Kahn, R.,Fieschi, F.
      (2008) Acta Crystallogr.,Sect.F 64: 115


    Organizational Affiliation

    Laboratoire des Proteines Membranaires, CEA, DSV, Institut de Biologie Structurale (IBS), Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 4 member K
A, B, C, D
156Homo sapiensMutation(s): 0 
Gene Names: CD207 (CLEC4K)
Find proteins for Q9UJ71 (Homo sapiens)
Go to Gene View: CD207
Go to UniProtKB:  Q9UJ71
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 79.555α = 90.00
b = 79.555β = 90.00
c = 90.144γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
XDSdata reduction
REFMACrefinement
Xnemodata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-24 
  • Released Date: 2009-01-27 
  • Deposition Author(s): Thepaut, M.

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance