4LNR

The structure of HLA-B*35:01 in complex with the peptide (RPQVPLRPMTY)

Summary for 4LNR

• Entry DOI: 10.2210/pdb4lnr/pdb
• Descriptor: HLA class I histocompatibility antigen, B-35 alpha chain, Beta-2-microglobulin, Peptide from Protein Nef, ... (4 entities in total)
• Functional Keywords: heterotrimer, ligand for t cell receptor, immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 45048.04

Authors

Cheng, H.,Shi, Y.,Qi, J.,Gao, G.F. (deposition date: 2013-07-12, release date: 2014-07-23, Last modification date: 2019-12-18)

Primary citation

Yanaka, S.,Ueno, T.,Shi, Y.,Qi, J.,Gao, G.F.,Tsumoto, K.,Sugase, K.
Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex.
J.Biol.Chem., 289:24680-24690, 2014

PubMed Abstract: In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8(+) T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an HLA class I allomorph in complex with HIV-derived peptides and evaluated site-specific conformational fluctuations using NMR. Although the crystal structures of various pHLAs were almost identical independent of the peptides, fluctuation analyses identified a peptide-dependent minor state that would be more tightly packed toward the peptide. The minor population correlated well with the thermostability and cell surface presentation of pHLA, indicating that this newly identified minor state is important for stabilizing the pHLA and facilitating T-cell recognition.

PubMed: 25028510
DOI: 10.1074/jbc.M114.566174

Experimental method

X-RAY DIFFRACTION (2 Å)