PDB 2IPK deposited: 2006-10-12 modified: 2009-02-24
Title Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2
Authors Bilsel, O., Chitta, S., Imperiali, B., Nguyen, T.T., Sainlos, M., Stern, L.J., Venkatraman, P.
Structure factors resolution 2.3 rfactor 0.203 rfree 0.224
DPI 0.59 theoretical min: 0.26

A crucial step in the immune response is the binding of antigenic peptides to major histocompatibility complex (MHC) proteins. Class II MHC proteins present their bound peptides to CD4(+) T cells, thereby helping to activate both the humoral and the cellular arms of the adaptive immune response. Peptide loading onto class II MHC proteins is regulated temporally, spatially and developmentally in antigen-presenting cells. To help visualize these processes, we have developed a series of novel fluorogenic probes that incorporate the environment-sensitive amino acid analogs 6-N,N-dimethylamino-2-3-naphthalimidoalanine and 4-N,N-dimethylaminophthalimidoalanine. Upon binding to class II MHC proteins these fluorophores show large changes in emission spectra, quantum yield and fluorescence lifetime. Peptides incorporating these fluorophores bind specifically to class II MHC proteins on antigen-presenting cells and can be used to follow peptide binding in vivo. Using these probes we have tracked a developmentally regulated cell-surface peptide-binding activity in primary human monocyte-derived dendritic cells.

Nat.Chem.Biol. 2007 Apr; 3(4):222-228 doi:10.1038/nchembio868

Cross References
Database source Identifier Description
ChEMBL Document CHEMBL1250445
PubMed 17351628
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
2IPK/1 2IPK 1 tetramer 0 4 0 5073