2IPK

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

Summary for 2IPK

• Entry DOI: 10.2210/pdb2ipk/pdb
• Related: 1DLH 1JWU
• Descriptor: HLA class II histocompatibility antigen, DR alpha chain, HLA class II histocompatibility antigen, DRB1-1 beta chain, HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine), ... (5 entities in total)
• Functional Keywords: hla, dr1, mhc, major histocompatibility complex, fluorogenic probe, sec3, 4-(n, n-dimethylamino)phthalimidoalanyl, dapa, immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Cell membrane; Single-pass type I membrane protein: P01903 P04229; Secreted: P0A0L3
• Total number of polymer chains: 4
• Total formula weight: 72848.96

Authors

Nguyen, T.T.,Stern, L.J. (deposition date: 2006-10-12, release date: 2007-03-13, Last modification date: 2023-08-30)

Primary citation

Venkatraman, P.,Nguyen, T.T.,Sainlos, M.,Bilsel, O.,Chitta, S.,Imperiali, B.,Stern, L.J.
Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells.
Nat.Chem.Biol., 3:222-228, 2007

PubMed Abstract: 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.

PubMed: 17351628
DOI: 10.1038/nchembio868

Experimental method

X-RAY DIFFRACTION (2.3 Å)