Primary Citation PubMed: 16007091
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Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors.
(2006) J Exp Med 203
PubMed: 16520393 | PubMedCentral: PMC2118257 | DOI: 10.1084/jem.20052369
Arg79 is conserved between mouse and human CD1d ( 17 , 18 ); however, comparison with the three currently available mouse CD1d structures ( 19 – 21 ) (accession nos. 1CD1, 1Z5L, and 1ZHN ) ind... ces that, certainly before TCR binding, this residue is conformationally very flexible (Fig.
Publication Year: 2006
Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity.
(2005) J Exp Med 202
PubMed: 16314439 | PubMedCentral: PMC2213337 | DOI: 10.1084/jem.20051625
The CD1d binding pocket is shown as a transparent molecular surface in a side view (top) or top view (bottom), either with (A) bound cis-teracosenoyl sulfatide (C 24:1 ) or with (B) the short-chain ... 003b1;-GalCer variant PBS-25 (PDB code 1Z5L).
Using the sitting drop vapor diffusion method, we crystallized the CD1d–sulfatide complex and determined its three-dimensional structure by molecular replacement using the protein coordinates of the CD1d short-chain α-GalCer complex (PDB code 1Z5L) as the search model ( Table I and Fig. 2 ; reference 11).
Publication Year: 2005
Invariant natural killer T cells recognize glycolipids from pathogenic Gram-positive bacteria.
(2011) Nat Immunol 12
PubMed: 21892173 | PubMedCentral: PMC3178673 | DOI: 10.1038/ni.2096
(c and d) Comparison of the hydrogen-bond network between CD1d and the ligands: (c) Glc-DAG-s2 yellow, α̃GalCer green, PDB code 1Z5L or (d) Glc-DAG-s2 yellow, BbGL-IIc cyan, PDB code 3... LQ.
Publication Year: 2011
Crystal structures of bovine CD1d reveal altered ?GalCer presentation and a restricted A' pocket unable to bind long-chain glycolipids.
(2012) PLoS One 7
PubMed: 23110152 | PubMedCentral: PMC3479135 | DOI: 10.1371/journal.pone.0047989
Superposition of the entire boCD1d heavy chain from the di-sulfatide complex with that of huCD1d and mCD1d yielded rmsd values of 0.92 Å (PDB 1ZT4) and 1.13 Å (PDB 1Z5L), respectively,... indicating a very similar topology of the boCD1d molecules.
Publication Year: 2012
Relationships between Th1 or Th2 iNKT cell activity and structures of CD1d-antigen complexes: meta-analysis of CD1d-glycolipids dynamics simulations.
(2014) PLoS Comput Biol 10
PubMed: 25376021 | PubMedCentral: PMC4222593 | DOI: 10.1371/journal.pcbi.1003902
These lipid structures have been taken from PDB files 3ARB  and 1Z5L.
For example, two X-ray structures (PDB references 3ARB and 1Z5L) show the presence of A′ and F′ pockets spacer lipids when CD1d is partially occupied by the sphingosin truncated 2 and the acyl truncated 6 analogues, respectively.
H_aGAL Sy1 1 2PO6 Human No Reference  ,  M_aGAL Sy2 3SDA Mouse  H_OCH Sy3 2 2PO6 Human PDB 3ARB Th2  M_OCH Sy4 3SDA Mouse  ,  H_OCH9 Sy5 3 2PO6 Human No Th2  H_7DW Sy6 4 2PO6 Human No Th1  M_7DW Sy7 3SDA Mouse  H_NUaGAL Sy8 5 2PO6 Human No Th1  M_NUaGAL Sy9 3SDA Mouse  ,  H_GOF Sy10 6 2PO6 Human from 1Z5L Th2  M_GOF Sy11 3SDA Mouse Th2  H_SaGAL Sy12 7 2PO6 Human No Th2  M_SaGAL Sy13 3SDA Mouse Inactive  M_AZOL Sy14 8 3SDA Mouse No Th2  H_CD1d Sy15 Lipid free 2PO6 Human No NA H_LIP Sy16 Two lipids 2PO6 Human PDB 3ARB&1Z5L NA Seven analogues of 1 have been chosen so as to account for modifications on the four portions of the glycolipid: the sugar part, the osidic bond, the polar linker, and the two lipid chains ( Figure 2 ).
The geometries of the analogues GOF, NUaGAL and OCH were taken from X-ray structures 1Z5L, 3QUZ and 3ARB, respectively.
Publication Year: 2014
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