3S6C

Structure of human CD1e


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human CD1e reveals a groove suited for lipid-exchange processes.

Garcia-Alles, L.F.Giacometti, G.Versluis, C.Maveyraud, L.de Paepe, D.Guiard, J.Tranier, S.Gilleron, M.Prandi, J.Hanau, D.Heck, A.J.Mori, L.De Libero, G.Puzo, G.Mourey, L.de la Salle, H.

(2011) Proc.Natl.Acad.Sci.USA 108: 13230-13235

  • DOI: 10.1073/pnas.1105627108

  • PubMed Abstract: 
  • CD1e is the only human CD1 protein existing in soluble form in the late endosomes of dendritic cells, where it facilitates the processing of glycolipid antigens that are ultimately recognized by CD1b-restricted T cells. The precise function of CD1e r ...

    CD1e is the only human CD1 protein existing in soluble form in the late endosomes of dendritic cells, where it facilitates the processing of glycolipid antigens that are ultimately recognized by CD1b-restricted T cells. The precise function of CD1e remains undefined, thus impeding efforts to predict the participation of this protein in the presentation of other antigens. To gain insight into its function, we determined the crystal structure of recombinant CD1e expressed in human cells at 2.90-Å resolution. The structure revealed a groove less intricate than in other CD1 proteins, with a significantly wider portal characterized by a 2 Å-larger spacing between the α1 and α2 helices. No electron density corresponding to endogenous ligands was detected within the groove, despite the presence of ligands unequivocally established by native mass spectrometry in recombinant CD1e. Our structural data indicate that the water-exposed CD1e groove could ensure the establishment of loose contacts with lipids. In agreement with this possibility, lipid association and dissociation processes were found to be considerably faster with CD1e than with CD1b. Moreover, CD1e was found to mediate in vitro the transfer of lipids to CD1b and the displacement of lipids from stable CD1b-antigen complexes. Altogether, these data support that CD1e could have evolved to mediate lipid-exchange/editing processes with CD1b and point to a pathway whereby the repertoire of lipid antigens presented by human dendritic cells might be expanded.


    Organizational Affiliation

    Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin, T-cell surface glycoprotein CD1e, membrane-associated
A
392Homo sapiensMutation(s): 0 
Gene Names: CD1E, B2M
Find proteins for P15812 (Homo sapiens)
Go to Gene View: CD1E
Go to UniProtKB:  P15812
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 206.289α = 90.00
b = 45.930β = 91.48
c = 65.628γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-08-31
    Type: Database references, Other
  • Version 1.2: 2017-08-23
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-08
    Type: Refinement description