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17  structures 142  species 2  interactions 300  sequences 8  architectures

Family: MHC2-interact (PF09307)

Summary: CLIP, MHC2 interacting

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

CLIP, MHC2 interacting Provide feedback

Members of this family are found in class II invariant chain-associated peptide (CLIP), and are required for association with class II major histocompatibility complex (MHC) in the MHC class II processing pathway [1].

Literature references

  1. Zhu Y, Rudensky AY, Corper AL, Teyton L, Wilson IA; , J Mol Biol. 2003;326:1157-1174.: Crystal structure of MHC class II I-Ab in complex with a human CLIP peptide: prediction of an I-Ab peptide-binding motif. PUBMED:12589760 EPMC:12589760


This tab holds annotation information from the InterPro database.

InterPro entry IPR015386

This domain is found in MHC class II-associated invariant chain (Ii), and in class II invariant chain-associated peptide (CLIP), and is required for association with class II major histocompatibility complex (MHC II) in the MHC II processing pathway [PUBMED:12589760]. Ii plays a critical role in the assembly of the MHC, as well as in MHC II antigen processing by stabilising peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to compartments where peptide loading of class II takes place [PUBMED:16337363]. In antigen-presenting cells (APCs), loading of MHC II molecules with peptides is regulated by Ii, which blocks MHC II antigen-binding sites in pre-endosomal compartments [PUBMED:16181341]. Several factors modulate the surface expression of MHC II molecules via post-Golgi mechanisms, including CLIP.

The Invariant chain contains a single transmembrane domain. Ii first assembles into a trimer and then associates with three class II alpha/beta MHC heterodimers. Although the membrane-proximal region of the Ii luminal domain is structurally disordered, the C-terminal segment of the luminal domain is largely alpha-helical and contains a major interaction site for the Ii trimer [PUBMED:9843486].

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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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(8)
Full
(300)
Representative proteomes UniProt
(503)
NCBI
(777)
Meta
(0)
RP15
(11)
RP35
(48)
RP55
(173)
RP75
(289)
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HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(8)
Full
(300)
Representative proteomes UniProt
(503)
NCBI
(777)
Meta
(0)
RP15
(11)
RP35
(48)
RP55
(173)
RP75
(289)
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
(8)
Full
(300)
Representative proteomes UniProt
(503)
NCBI
(777)
Meta
(0)
RP15
(11)
RP35
(48)
RP55
(173)
RP75
(289)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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.

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: pdb_1muj
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Sammut SJ
Number in seed: 8
Number in full: 300
Average length of the domain: 107.80 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 43.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.9 26.9
Trusted cut-off 27.0 27.1
Noise cut-off 26.4 26.6
Model length: 109
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 2 interactions for this family. More...

MHC_II_alpha MHC_II_beta

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 MHC2-interact domain has been found. There are 17 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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