3C22 | pdb_00003c22

Crystal structure of the carbohydrate recognition domain of human Langerin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.236 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3C22

This is version 1.2 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: https://doi.org/10.1021/bi802151w
  • Primary Citation Related Structures: 
    3C22

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 72.1 kDa 
  • Atom Count: 5,340 
  • Modeled Residue Count: 523 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member K
A, B, C, D
156Homo sapiensMutation(s): 0 
Gene Names: CD207
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ71 (Homo sapiens)
Explore Q9UJ71 
Go to UniProtKB:  Q9UJ71
PHAROS:  Q9UJ71
GTEx:  ENSG00000116031 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJ71
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C],
M [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]
H [auth B]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.236 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.555α = 90
b = 79.555β = 90
c = 90.144γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Xnemodata collection
XDSdata reduction
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary