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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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Alignments

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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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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:
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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.

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: 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...

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

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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