Summary: Immunoglobulin I-set domain
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Immunoglobulin I-set domain Edit Wikipedia article
|Immunoglobulin I-set domain|
Structures of fibroblast growth factor 1.
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, and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.
Human proteins containing this domain
- ADAMTSL1, ADAMTSL3, ALPK3, AXL,
- C9orf94, CADM2, CADM4, CCDC141, CDON, CEACAM7, CHL1, CILP2, CNTN1, CNTN2, CNTN3, CNTN4, CNTN5, CNTN6, CXADR,
- DCC, DSCAM, DSCAML1,
- FGFR1, FGFR3, FGFR4, FGFRL1, FLT1, FLT4, FSTL4, FSTL5,
- HMCN1, HNT, HSPG2,
- ICAM5, IGFBP7, IGFBPL1, IGSF10, IGSF22, IGSF9, ISLR,
- KALRN, KAZALD1, KDR, KIAA0626, KIRREL, KIRREL2, KIRREL3,
- L1CAM, LINGO1, LINGO2, LRFN2, LRFN3, LRFN4, LRFN5, LRIG1, LRIG2, LRIG3, LRIT2, LRIT3, LRRC24, LRRC4B, LRRC4C, LRRN1, LRRN3, LRRN5, LSAMP,
- MAG, MDGA2, MFAP3L, MUSK, MXRA5, MYBPC1, MYBPC2, MYBPC3, MYBPH, MYBPHL, MYLK, MYOM1, MYOM2, MYOM3, MYOT, MYPN,
- NCAM1, NCAM2, NEGR1, NEO1, NEXN, NFASC, NGL1, NOPE, NPHS1, NPTN, NRCAM, NRG2, NT[disambiguation needed], NTRK2, NTRK3,
- OBSCN, OBSL1, OPCML,
- PALLD, PAPLN, PDGFRA, PRODH2, PTK7, PTPRD, PTPRF, PTPRS, PTPsigma, PUNC,
- ROBO1, ROBO2, ROBO3, ROBO4, ROR1, ROR2,
- SDK1, SDK2, SIGLEC1, SIGLEC6, SPEG,
- TRIO, TTN,
- UNC5A, UNC5B, UNC5C,
- VCAM1, WFIKKN1, WFIKKN2,
- 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.
- 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.
- 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.
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Immunoglobulin I-set domain Provide feedback
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Internal database links
|SCOOP:||V-set V-set_CD47 C2-set_2 Receptor_2B4 Ig_2 Ig_3 V-set_2 Ig_4 Ig_5 Izumo-Ig UL141|
|Similarity to PfamA using HHSearch:||ig C1-set V-set V-set_CD47 C2-set_2 Receptor_2B4 Ig_2 Ig_3 Ig_4 Ig_5 Izumo-Ig|
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].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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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 . 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 . 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 28 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_4 Ig_5 Ig_Tie2_1 Izumo-Ig K1 Lep_receptor_Ig Marek_A PTCRA Receptor_2B4 SVA UL141 V-set V-set_2 V-set_CD47
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||48|
|Number in full:||84215|
|Average length of the domain:||88.50 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||29.38 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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There are 25 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 451 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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