1ONQ

Crystal Structure of CD1a in Complex with a Sulfatide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A.

Zajonc, D.M., Elsliger, M.A., Teyton, L., Wilson, I.A.

(2003) Nat.Immunol. 4: 808-815

  • DOI: 10.1038/ni948

  • PubMed Abstract: 

    • CD1 antigens bind a variety of self and foreign lipid and glycolipid antigens for presentation to CD1-restricted T cell receptors (TCRs). Here we report the crystal structure of human CD1a in complex with a sulfatide self antigen at a resolution of 2 ...

    CD1 antigens bind a variety of self and foreign lipid and glycolipid antigens for presentation to CD1-restricted T cell receptors (TCRs). Here we report the crystal structure of human CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A. The lipid adopts an S-shaped conformation, with the sphingosine chain completely buried in the A' pocket and the fatty acid chain emerging from the interface of the A' pocket into the more exposed F' pocket. The headgroup is anchored in the A'-F' junction and protrudes into the F' pocket for TCR recognition. Because the A' pocket is narrow with a fixed terminus, it can act as a molecular 'ruler' to select alkyl chains of a particular length.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1a
A, C
283Homo sapiensMutation(s): 0 
Gene Names: CD1A
Find proteins for P06126 (Homo sapiens)
Go to Gene View: CD1A
Go to UniProtKB:  P06126
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Homo sapiensMutation(s): 0 
Gene Names: B2M
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
SLF
Query on SLF
Download SDF File 
Download CCD File 
A, C
SULFATE-3-D-GALACTOSYL-BETA-1-1-N-STEAROYL-D-SPHINGOSINE
C42 H81 N O11 S
GQQZXRPXBDJABR-BDZNYNMQSA-N
 Ligand Interaction
FUC
Query on FUC
Download SDF File 
Download CCD File 
A, C
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.407α = 90.00
b = 42.711β = 90.78
c = 204.217γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance