Summary: CLIP, MHC2 interacting
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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 .
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
External database links
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].
More information about these proteins can be found at Protein of the Month: MHC [PUBMED:].
|Cellular component||membrane (GO:0016020)|
|Molecular function||MHC class II protein binding (GO:0042289)|
|Biological process||intracellular protein transport (GO:0006886)|
|antigen processing and presentation (GO:0019882)|
|immune response (GO:0006955)|
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Curation and family details
|Author:||Mistry J, Sammut SJ|
|Number in seed:||11|
|Number in full:||121|
|Average length of the domain:||111.30 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||44.98 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
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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 11 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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