1ZT4

The crystal structure of human CD1d with and without alpha-Galactosylceramide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of human CD1d with and without alpha-galactosylceramide

Koch, M.Stronge, V.S.Shepherd, D.Gadola, S.D.Mathew, B.Ritter, G.Fersht, A.R.Besra, G.S.Schmidt, R.R.Jones, E.Y.Cerundolo, V.

(2005) Nat.Immunol. 6: 819-826

  • DOI: 10.1038/ni1225

  • PubMed Abstract: 
  • The glycolipid alpha-galactosylceramide binds with high affinity to CD1d and stimulates natural killer T cells. Here we report the crystal structure of human CD1d in complex with synthetic alpha-galactosylceramide at a resolution of 3.0 A. The struct ...

    The glycolipid alpha-galactosylceramide binds with high affinity to CD1d and stimulates natural killer T cells. Here we report the crystal structure of human CD1d in complex with synthetic alpha-galactosylceramide at a resolution of 3.0 A. The structure shows a tightly fit lipid in the CD1d binding groove, with the sphingosine chain bound in the C' pocket and the longer acyl chain anchored in the A' pocket. We also present the CD1d structure without lipid, which has a more open conformation of the binding groove, suggesting a dual conformation of CD1d in which the 'open' conformation is more able to load lipids. These structures provide clues as to how CD1 molecules load glycolipids as well as data to guide the design of new therapeutic agents.


    Organizational Affiliation

    Cancer Research UK Receptor Structure Research Group, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Headington, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1d
A, C
281Homo sapiensGene Names: CD1D
Find proteins for P15813 (Homo sapiens)
Go to Gene View: CD1D
Go to UniProtKB:  P15813
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
100Homo sapiensGene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGH
Query on AGH

Download SDF File 
Download CCD File 
A
N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.470α = 90.00
b = 94.300β = 90.00
c = 176.070γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance