The domain within your query sequence starts at position 1 and ends at position 42; the E-value for the MHC_II_beta domain shown below is 8e-12.

MFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGA

MHC_II_beta

MHC_II_beta
PFAM accession number:PF00969
Interpro abstract (IPR000353):

Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response.

Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection) [(PUBMED:15120183)].

MHC class II molecules are comprised of two membrane-spanning chains, alpha and beta, of similar size. Both chains consist of two globular domains (N- and C-terminal), and a transmembrane segment to anchor them to the membrane [(PUBMED:7612235)]. A groove in the structure acts as the peptide-binding site.

This entry represents the N-terminal domain (also called beta-1 domain) of the beta chain.

GO process:antigen processing and presentation (GO:0019882), immune response (GO:0006955)
GO component:MHC class II protein complex (GO:0042613), membrane (GO:0016020)

This is a PFAM domain. For full annotation and more information, please see the PFAM entry MHC_II_beta