Summary: Immunoglobulin I-set domain
This is the Wikipedia entry entitled "Immunoglobulin I-set domain". More...
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Immunoglobulin I-set domain Edit Wikipedia article
|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
|Similarity to PfamA using HHSearch:||ig BiPBP_C C1-set V-set V-set_CD47 C2-set_2 Ig_2 Ig_3|
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].
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Curation and family details
|Seed source:||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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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There are 8 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 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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