2IPK image
Deposition Date 2006-10-12
Release Date 2007-03-13
Last Version Date 2023-08-30
Entry Detail
PDB ID:
2IPK
Keywords:
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
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.22
Space Group:
H 3
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:HLA class II histocompatibility antigen, DR alpha chain
Gene (Uniprot):HLA-DRA
Chain IDs:A
Chain Length:183
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:HLA class II histocompatibility antigen, DRB1-1 beta chain
Chain IDs:B
Chain Length:190
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine)
Chain IDs:C
Chain Length:14
Number of Molecules:1
Biological Source:Influenza A virus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Enterotoxin type C-3
Mutagens:K70S, L72F, A73K, H74W
Chain IDs:D
Chain Length:240
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus Mu50
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4DP C TRP ?
Primary Citation
Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells.
Nat.Chem.Biol. 3 222 228 (2007)
PMID: 17351628 DOI: 10.1038/nchembio868

Abstact

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.

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Primary Citation of related structures