6LUO

Structure of nurse shark beta-2-microglobulin

Summary for 6LUO

• Entry DOI: 10.2210/pdb6luo/pdb
• Descriptor: Beta-2-microglobulin (2 entities in total)
• Functional Keywords: nurse shark, monomer beta-2-microglobulin, mhc class i, immune system
• Biological source: Ginglymostoma cirratum (Nurse shark)
• Total number of polymer chains: 2
• Total formula weight: 22078.66

Authors

Xia, C.,Wu, Y. (deposition date: 2020-01-30, release date: 2021-04-28, Last modification date: 2023-11-29)

Primary citation

Wu, Y.,Zhang, N.,Wei, X.,Lu, S.,Li, S.,Hashimoto, K.,Dijkstra, J.M.,Xia, C.
The Structure of a Peptide-Loaded Shark MHC Class I Molecule Reveals Features of the Binding between beta 2 -Microglobulin and H Chain Conserved in Evolution.
J Immunol., 2021

PubMed Abstract: Cartilaginous fish are the most primitive extant species with MHC molecules. Using the nurse shark, the current study is, to the best of our knowledge, the first to present a peptide-loaded MHC class I (pMHC-I) structure for this class of animals. The overall structure was found to be similar between cartilaginous fish and bony animals, showing remarkable conservation of interactions between the three pMHC-I components H chain, β-microglobulin (β-m), and peptide ligand. In most previous studies, relatively little attention was given to the details of binding between the H chain and β-m, and our study provides important new insights. A pronounced conserved feature involves the insertion of a large β-m F56+W60 hydrophobic knob into a pleat of the β-sheet floor of the H chain α1α2 domain, with the knob being surrounded by conserved residues. Another conserved feature is a hydrogen bond between β-m Y10 and a proline in the α3 domain of the H chain. By alanine substitution analysis, we found that the conserved β-m residues Y10, D53, F56, and W60-each binding the H chain-are required for stable pMHC-I complex formation. For the β-m residues Y10 and F56, such observations have not been reported before. The combined data indicate that for stable pMHC-I complex formation β-m should not only bind the α1α2 domain but also the α3 domain. Knowing the conserved structural features of pMHC-I should be helpful for future elucidations of the mechanisms of pMHC-I complex formation and peptide editing.

PubMed: 34145057
DOI: 10.4049/jimmunol.2001165

Experimental method

X-RAY DIFFRACTION (2.302 Å)