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741  structures 689  species 0  interactions 379774  sequences 9851  architectures

Family: I-set (PF07679)

Summary: Immunoglobulin I-set domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Immunoglobulin I-set domain Edit Wikipedia article

Immunoglobulin I-set domain
Identifiers
SymbolI-set
PfamPF07679
InterProIPR013098

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[1], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis[2].

Human proteins containing this domain

ADAMTSL1; ADAMTSL3; ALPK3; AXL; BOC; C9orf94; CADM2; CADM4; CCDC141; CDON; CEACAM7; CHL1; CILP2; CNTN1; CNTN2; CNTN3; CNTN4; CNTN5; CNTN6; CXADR; DCC; DSCAM; DSCAML1; ESAM; 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; 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;

References

  1. ^ 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): -. PMID 10830169.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ 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: -. PMID 16369100.{{cite journal}}: CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR013098

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Immunoglobulin I-set domain Provide feedback

No Pfam abstract.

Internal 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 ], the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [ PUBMED:16369100 ] and the Zwei Ig domain proteins zig involved in the postembriogenic neuronal soma and axon position maintenance [ PUBMED:11809975 , PUBMED:22829780 ].

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 34 members:

Adeno_E3_CR1 Adhes-Ig_like bCoV_NS7A bCoV_NS8 C1-set C2-set C2-set_2 CD4-extracel DUF1968 Herpes_gE Herpes_gI Herpes_glycop_D I-set ICAM_N ig Ig_2 Ig_3 Ig_4 Ig_5 Ig_6 Ig_7 Ig_C17orf99 Ig_C19orf38 Ig_Tie2_1 Izumo-Ig K1 Marek_A ObR_Ig PTCRA Receptor_2B4 UL141 V-set V-set_2 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(379774)
Representative proteomes UniProt
(579471)
RP15
(43389)
RP35
(115132)
RP55
(274355)
RP75
(381589)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(48)
Full
(379774)
Representative proteomes UniProt
(579471)
RP15
(43389)
RP35
(115132)
RP55
(274355)
RP75
(381589)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(379774)
Representative proteomes UniProt
(579471)
RP15
(43389)
RP35
(115132)
RP55
(274355)
RP75
(381589)
Raw Stockholm Download     Download   Download   Download      
Gzipped Download     Download   Download   Download      

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 48
Number in full: 379774
Average length of the domain: 88.7 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 25.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -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: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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 741 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044QKH1 View 3D Structure Click here
A0A044QQM7 View 3D Structure Click here
A0A044R9D0 View 3D Structure Click here
A0A044RYL9 View 3D Structure Click here
A0A044S247 View 3D Structure Click here
A0A044S2H5 View 3D Structure Click here
A0A044S4W0 View 3D Structure Click here
A0A044SKA2 View 3D Structure Click here
A0A044SX34 View 3D Structure Click here
A0A044T3B3 View 3D Structure Click here
A0A044T3S7 View 3D Structure Click here
A0A044T607 View 3D Structure Click here
A0A044TBE7 View 3D Structure Click here
A0A044TD32 View 3D Structure Click here
A0A044TG54 View 3D Structure Click here
A0A044TGP3 View 3D Structure Click here
A0A044TJ59 View 3D Structure Click here
A0A044TL59 View 3D Structure Click here
A0A044TP14 View 3D Structure Click here
A0A044TPB0 View 3D Structure Click here
A0A044U4T6 View 3D Structure Click here
A0A044U682 View 3D Structure Click here
A0A044UGZ6 View 3D Structure Click here
A0A044UIA8 View 3D Structure Click here
A0A044UZ90 View 3D Structure Click here
A0A044VJ14 View 3D Structure Click here
A0A077YVH5 View 3D Structure Click here
A0A077YZ00 View 3D Structure Click here
A0A077YZT2 View 3D Structure Click here
A0A077Z0D0 View 3D Structure Click here
A0A077Z1Z5 View 3D Structure Click here
A0A077Z2G9 View 3D Structure Click here
A0A077Z2W6 View 3D Structure Click here
A0A077Z2X9 View 3D Structure Click here
A0A077Z2Y8 View 3D Structure Click here
A0A077Z3G5 View 3D Structure Click here
A0A077Z3H0 View 3D Structure Click here
A0A077Z3S0 View 3D Structure Click here
A0A077Z439 View 3D Structure Click here
A0A077Z450 View 3D Structure Click here