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375  structures 1617  species 8  interactions 59728  sequences 3030  architectures

Family: I-set (PF07679)

Summary: Immunoglobulin I-set domain

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This is the Wikipedia entry entitled "Immunoglobulin I-set domain". More...

Immunoglobulin I-set domain Edit Wikipedia article

Immunoglobulin I-set domain
PDB 1evt EBI.jpg
Structures of fibroblast growth factor 1.[1]
Identifiers
Symbol I-set
Pfam PF07679
InterPro IPR013098

I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1,[2] and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.[3]

Human proteins containing this domain[edit]

References[edit]

  1. ^ Plotnikov AN, Hubbard SR, Schlessinger J, Mohammadi M (May 2000). "Crystal structures of two FGF-FGFR complexes reveal the determinants of ligand-receptor specificity". Cell 101 (4): 413–24. doi:10.1016/S0092-8674(00)80851-X. PMID 10830168. 
  2. ^ Sonderegger P, Welte W, Diederichs K, Freigang J, Proba K, Leder L (2000). "The crystal structure of the ligand binding module of axonin-1/TAG-1 suggests a zipper mechanism for neural cell adhesion". Cell 101 (4): 425–33. doi:10.1016/S0092-8674(00)80852-1. PMID 10830169. 
  3. ^ Stuart DI, Jones EY, Harlos K, Esnouf RM, Love CA (2006). "Structure determination of human semaphorin 4D as an example of the use of MAD in non-optimal cases". Acta Crystallogr. D 62 (Pt 1): 108–15. doi:10.1107/S0907444905034992. PMID 16369100. 

This article incorporates text from the public domain Pfam and InterPro IPR013098


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Immunoglobulin I-set domain Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013098

The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; INTERPRO), C1-set (constant-1; INTERPRO), C2-set (constant-2; INTERPRO) and I-set (intermediate; INTERPRO) [PUBMED:9417933]. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [PUBMED:15327963, PUBMED:11377196].

Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system [PUBMED:10698639].

This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [PUBMED:10830169], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [PUBMED:16369100].

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 Ig (CL0011), which has the following description:

Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The superfamily can be divided into discrete structural sets, by the presence or absence of beta-strands in the structure and the length of the domains [1]. Proteins containing domains of the C1 and V-sets are mostly molecules of the vertebrate immune system. Proteins of the C2-set are mainly lymphocyte antigens, this differs from the composition of the C2-set as originally proposed [1]. The I-set is intermediate in structure between the C1 and V-sets and is found widely in cell surface proteins as well as intracellular muscle proteins.

The clan contains the following 24 members:

A2M Adeno_E3_CR1 Adhes-Ig_like C1-set C2-set C2-set_2 Herpes_gE Herpes_gI Herpes_glycop_D I-set ICAM_N ig Ig_2 Ig_3 Ig_Tie2_1 IZUMO K1 Lep_receptor_Ig Marek_A PTCRA Receptor_2B4 SVA V-set V-set_CD47

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
(48)
Full
(59728)
Representative proteomes NCBI
(71682)
Meta
(78)
RP15
(6694)
RP35
(9324)
RP55
(18688)
RP75
(30033)
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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
(48)
Full
(59728)
Representative proteomes NCBI
(71682)
Meta
(78)
RP15
(6694)
RP35
(9324)
RP55
(18688)
RP75
(30033)
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
(48)
Full
(59728)
Representative proteomes NCBI
(71682)
Meta
(78)
RP15
(6694)
RP35
(9324)
RP55
(18688)
RP75
(30033)
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.

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.

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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 48
Number in full: 59728
Average length of the domain: 88.50 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 29.33 %

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 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.6 23.6
Model length: 90
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 8 interactions for this family. More...

Telethonin LRR_1 ig FGF I-set C2-set Pkinase fn3

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 I-set domain has been found. There are 375 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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