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721  structures 609  species 0  interactions 246980  sequences 8395  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

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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...

View options

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
(246980)
Representative proteomes UniProt
(496724)
RP15
(35951)
RP35
(110042)
RP55
(245928)
RP75
(340014)
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HTML View             
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
(246980)
Representative proteomes UniProt
(496724)
RP15
(35951)
RP35
(110042)
RP55
(245928)
RP75
(340014)
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
(246980)
Representative proteomes UniProt
(496724)
RP15
(35951)
RP35
(110042)
RP55
(245928)
RP75
(340014)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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.

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: 246980
Average length of the domain: 88.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 24.46 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 721 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
A0A087WV53 View 3D Structure Click here
A0A087WV53 View 3D Structure Click here
A0A0B4J1L0 View 3D Structure Click here
A0A0B4K6Z6 View 3D Structure Click here
A0A0B4K6Z6 View 3D Structure Click here
A0A0B4K6Z6 View 3D Structure Click here
A0A0B4K6Z6 View 3D Structure Click here
A0A0B4K6Z6 View 3D Structure Click here
A0A0B4LI09 View 3D Structure Click here
A0A0B4LI09 View 3D Structure Click here
A0A0C4DHN4 View 3D Structure Click here
A0A0G2JSU2 View 3D Structure Click here
A0A0G2JVW0 View 3D Structure Click here
A0A0G2JZA1 View 3D Structure Click here
A0A0G2JZA1 View 3D Structure Click here
A0A0G2JZA1 View 3D Structure Click here
A0A0G2JZA1 View 3D Structure Click here
A0A0G2K046 View 3D Structure Click here
A0A0G2K046 View 3D Structure Click here
A0A0G2K046 View 3D Structure Click here
A0A0G2K046 View 3D Structure Click here
A0A0G2K046 View 3D Structure Click here
A0A0G2K210 View 3D Structure Click here
A0A0G2K210 View 3D Structure Click here
A0A0G2K320 View 3D Structure Click here
A0A0G2K320 View 3D Structure Click here
A0A0G2K320 View 3D Structure Click here
A0A0G2K5P5 View 3D Structure Click here
A0A0G2K5P5 View 3D Structure Click here
A0A0G2K5P5 View 3D Structure Click here
A0A0G2K5P5 View 3D Structure Click here
A0A0G2K7P9 View 3D Structure Click here
A0A0G2K7P9 View 3D Structure Click here
A0A0G2K7P9 View 3D Structure Click here
A0A0G2K7P9 View 3D Structure Click here
A0A0G2K994 View 3D Structure Click here
A0A0G2K999 View 3D Structure Click here
A0A0G2K999 View 3D Structure Click here
A0A0G2K999 View 3D Structure Click here
A0A0G2K999 View 3D Structure Click here
A0A0G2KHM6 View 3D Structure Click here
A0A0G2KHM6 View 3D Structure Click here
A0A0G2KHM6 View 3D Structure Click here
A0A0G2KHM6 View 3D Structure Click here
A0A0G2KR08 View 3D Structure Click here
A0A0G2KSM2 View 3D Structure Click here
A0A0G2KXQ3 View 3D Structure Click here
A0A0G2L9T1 View 3D Structure Click here
A0A0G2LAI5 View 3D Structure Click here
A0A0G2LAI5 View 3D Structure Click here
A0A0H2UKQ6 View 3D Structure Click here
A0A0H2UKQ6 View 3D Structure Click here
A0A0H2UKQ6 View 3D Structure Click here
A0A0H2UKQ6 View 3D Structure Click here
A0A0H2UKT5 View 3D Structure Click here
A0A0H2UKT5 View 3D Structure Click here
A0A0H2UKW5 View 3D Structure Click here
A0A0R4IAW3 View 3D Structure Click here
A0A0R4IAW3 View 3D Structure Click here
A0A0R4IBA6 View 3D Structure Click here
A0A0R4IBM0 View 3D Structure Click here
A0A0R4ICM3 View 3D Structure Click here
A0A0R4IDE1 View 3D Structure Click here
A0A0R4IDE1 View 3D Structure Click here
A0A0R4IDE1 View 3D Structure Click here
A0A0R4IDE1 View 3D Structure Click here
A0A0R4IE04 View 3D Structure Click here
A0A0R4IEH4 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGP9 View 3D Structure Click here
A0A0R4IGQ8 View 3D Structure Click here
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A0A0R4IGQ8 View 3D Structure Click here
A0A0R4IGQ8 View 3D Structure Click here
A0A0R4IHP4 View 3D Structure Click here
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A0A0R4IP15 View 3D Structure Click here
A0A0R4IP15 View 3D Structure Click here
A0A0R4IP15 View 3D Structure Click here
A0A0R4IR64 View 3D Structure Click here
A0A0R4IRX5 View 3D Structure Click here
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A0A0R4ITG7 View 3D Structure Click here
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A0A0R4ITG7 View 3D Structure Click here
A0A0R4ITG7 View 3D Structure Click here
A0A0R4ITX7 View 3D Structure Click here
A0A0R4IX71 View 3D Structure Click here
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A0A0R4IXF4 View 3D Structure Click here
A0A0R4IZ74 View 3D Structure Click here
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A0A0R4IZB7 View 3D Structure Click here
A0A140LHZ9 View 3D Structure Click here
A0A1D5NS30 View 3D Structure Click here
A0A1D5NS30 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1L1QZU5 View 3D Structure Click here
A0A1W2Q6M9 View 3D Structure Click here
A0A286Y8D8 View 3D Structure Click here
A0A286YAB9 View 3D Structure Click here
A0A2R8PYK8 View 3D Structure Click here
A0A2R8PZW4 View 3D Structure Click here
A0A2R8PZW4 View 3D Structure Click here
A0A2R8PZW4 View 3D Structure Click here
A0A2R8PZW4 View 3D Structure Click here
A0A2R8Q0Z9 View 3D Structure Click here
A0A2R8Q0Z9 View 3D Structure Click here
A0A2R8Q376 View 3D Structure Click here
A0A2R8Q4J6 View 3D Structure Click here
A0A2R8Q5B6 View 3D Structure Click here
A0A2R8Q679 View 3D Structure Click here
A0A2R8Q679 View 3D Structure Click here
A0A2R8Q7H4 View 3D Structure Click here
A0A2R8Q7M4 View 3D Structure Click here
A0A2R8Q7U1 View 3D Structure Click here
A0A2R8Q7U1 View 3D Structure Click here
A0A2R8Q9N4 View 3D Structure Click here
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A0A2R8QBU4 View 3D Structure Click here
A0A2R8QCX6 View 3D Structure Click here
A0A2R8QDF4 View 3D Structure Click here
A0A2R8QHB4 View 3D Structure Click here
A0A2R8QHE8 View 3D Structure Click here
A0A2R8QHE8 View 3D Structure Click here
A0A2R8QHN1 View 3D Structure Click here
A0A2R8QJT8 View 3D Structure Click here
A0A2R8QJT8 View 3D Structure Click here
A0A2R8QJT8 View 3D Structure Click here
A0A2R8QJT8 View 3D Structure Click here
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A0A2R8QLU2 View 3D Structure Click here
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A0A2R8QLU2 View 3D Structure Click here
A0A2R8QPT5 View 3D Structure Click here
A0A2R8QRK0 View 3D Structure Click here
A0A2R8QRK0 View 3D Structure Click here
A0A2R8QRQ4 View 3D Structure Click here
A0A2R8QRQ4 View 3D Structure Click here
A0A2R8RME3 View 3D Structure Click here
A0A2R8RME3 View 3D Structure Click here
A0A2R8RMY1 View 3D Structure Click here
A0A2R8RN55 View 3D Structure Click here
A0A2R8RN55 View 3D Structure Click here
A0A2R8RN55 View 3D Structure Click here
A0A2R8RQ37 View 3D Structure Click here
A0A2R9YJN4 View 3D Structure Click here
A0A4W4 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A0A571BEN1 View 3D Structure Click here
A1KZ92 View 3D Structure Click here
A1KZ92 View 3D Structure Click here
A1KZ92 View 3D Structure Click here
A1Z6H9 View 3D Structure Click here
A1Z920 View 3D Structure Click here
A1Z920 View 3D Structure Click here
A1Z9G5 View 3D Structure Click here
A1Z9X4 View 3D Structure Click here
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A1ZAB1 View 3D Structure Click here
A1ZBY3 View 3D Structure Click here
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A2ABU4 View 3D Structure Click here
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A2RUH7 View 3D Structure Click here
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A3KH16 View 3D Structure Click here
A4IFW2 View 3D Structure Click here
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A4IFW2 View 3D Structure Click here
A4IJ70 View 3D Structure Click here
A4JYK0 View 3D Structure Click here
A4JYK9 View 3D Structure Click here
A4JYK9 View 3D Structure Click here
A4JYK9 View 3D Structure Click here
A4JYL4 View 3D Structure Click here
A5I9F0 View 3D Structure Click here
A5WVM1 View 3D Structure Click here
A6H8Q3 View 3D Structure Click here
A6H8Q3 View 3D Structure Click here
A6NMB1 View 3D Structure Click here
A7IT77 View 3D Structure Click here
A8JNC7 View 3D Structure Click here
A8JNC7 View 3D Structure Click here
A8KB32 View 3D Structure Click here
A8WG19 View 3D Structure Click here
A8WGA3 View 3D Structure Click here
A9JRH0 View 3D Structure Click here
A9JRY6 View 3D Structure Click here
A9JST8 View 3D Structure Click here
B0BN16 View 3D Structure Click here
B0BNK7 View 3D Structure Click here
B0CLV6 View 3D Structure Click here
B0CM22 View 3D Structure Click here
B0S595 View 3D Structure Click here
B0S5R7 View 3D Structure Click here
B0S755 View 3D Structure Click here
B0V1B1 View 3D Structure Click here
B0V2N1 View 3D Structure Click here
B0V2N1 View 3D Structure Click here
B0V2N1 View 3D Structure Click here
B1H232 View 3D Structure Click here
B1Q236 View 3D Structure Click here
B2RSG7 View 3D Structure Click here
B3DH26 View 3D Structure Click here
B3DHL7 View 3D Structure Click here
B3DIC8 View 3D Structure Click here
B3DKP1 View 3D Structure Click here
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B4F6P2 View 3D Structure Click here
B7Z153 View 3D Structure Click here
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B8A5K6 View 3D Structure Click here
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B8JI51 View 3D Structure Click here
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B8JLJ1 View 3D Structure Click here
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C6KRM7 View 3D Structure Click here
C6KRM7 View 3D Structure Click here
D3YX43 View 3D Structure Click here
D3YYU8 View 3D Structure Click here
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D3Z874 View 3D Structure Click here
D3Z874 View 3D Structure Click here
D3Z874 View 3D Structure Click here
D3Z9K5 View 3D Structure Click here
D3Z9T4 View 3D Structure Click here
D3ZA38 View 3D Structure Click here
D3ZA38 View 3D Structure Click here
D3ZA38 View 3D Structure Click here
D3ZA38 View 3D Structure Click here
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D3ZAV8 View 3D Structure Click here
D3ZD40 View 3D Structure Click here
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D3ZD84 View 3D Structure Click here
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D3ZD96 View 3D Structure Click here
D3ZEY0 View 3D Structure Click here
D3ZFU9 View 3D Structure Click here
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D3ZH28 View 3D Structure Click here
D3ZHG3 View 3D Structure Click here
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D3ZJ81 View 3D Structure Click here
D3ZKA2 View 3D Structure Click here
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D3ZKA2 View 3D Structure Click here
D3ZNY8 View 3D Structure Click here
D3ZPL7 View 3D Structure Click here
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