Summary: Class II histocompatibility antigen, beta domain
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Class II histocompatibility antigen, beta domain Provide feedback
No Pfam abstract.
Literature references
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Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, Wiley DC; , Nature 1994;368:215-221.: Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. PUBMED:8145819 EPMC:8145819
Internal database links
SCOOP: | MHC_I MHC_I_3 |
External database links
HOMSTRAD: | MHC_II_N MHC_II_beta_NC |
SCOP: | 1seb |
This tab holds annotation information from the InterPro database.
InterPro entry 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.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
MHC class II protein complex (GO:0042613) | |
Biological process | antigen processing and presentation (GO:0019882) |
immune response (GO:0006955) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
Alignments
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Seed (27) |
Full (1693) |
Representative proteomes | UniProt (42122) |
NCBI (34741) |
Meta (0) |
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RP15 (85) |
RP35 (236) |
RP55 (744) |
RP75 (1495) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (27) |
Full (1693) |
Representative proteomes | UniProt (42122) |
NCBI (34741) |
Meta (0) |
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RP15 (85) |
RP35 (236) |
RP55 (744) |
RP75 (1495) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_331 (release 3.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 27 |
Number in full: | 1693 |
Average length of the domain: | 73.30 aa |
Average identity of full alignment: | 35 % |
Average coverage of the sequence by the domain: | 28.92 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 75 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 25 interactions for this family. More...
MHC_II_beta Hemagglutinin Stap_Strp_tox_C Gag_p24 DNA_pol_B MA-Mit Lectin_C MHC2-interact V-set C1-set MHC_II_alpha MHC_I Transferrin V-set TIM DUF1968 C1-set Stap_Strp_tox_C DUF1968 GTP_EFTU_D3 Cytochrom_C MHC_II_alpha Integrin_beta Myelin_MBP MLANAStructures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the MHC_II_beta domain has been found. There are 299 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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