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142  structures 277  species 6  interactions 3084  sequences 5  architectures

Family: MHC_II_alpha (PF00993)

Summary: Class II histocompatibility antigen, alpha domain

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Class II histocompatibility antigen, alpha domain Provide feedback

No Pfam abstract.

Literature references

  1. 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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001003

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 alpha-1 domain) of the alpha chain.

More information about these proteins can be found at Protein of the Month: MHC [PUBMED:].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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

This family is a member of clan MHC (CL0343), which contains the following 4 members:

MHC_I MHC_I_2 MHC_II_alpha MHC_II_beta

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(51)
Full
(3084)
Representative proteomes NCBI
(2606)
Meta
(0)
RP15
(7)
RP35
(18)
RP55
(38)
RP75
(138)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(51)
Full
(3084)
Representative proteomes NCBI
(2606)
Meta
(0)
RP15
(7)
RP35
(18)
RP55
(38)
RP75
(138)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(51)
Full
(3084)
Representative proteomes NCBI
(2606)
Meta
(0)
RP15
(7)
RP35
(18)
RP55
(38)
RP75
(138)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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 View help on the curation process

Seed source: Pfam-B_1288 (release 3.0)
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A, Griffiths-Jones SR
Number in seed: 51
Number in full: 3084
Average length of the domain: 76.50 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 55.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.8 20.6
Noise cut-off 20.5 20.4
Model length: 82
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 6 interactions for this family. More...

MA-Mit Stap_Strp_tox_C C1-set MHC_II_alpha MHC_II_beta Stap_Strp_toxin

Structures

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_alpha domain has been found. There are 142 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 seqence.

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