Summary: Immunoglobulin C1-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 C1-set domain". More...
Immunoglobulin C1-set domain Edit Wikipedia article
Immunoglobulin C1-set domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() Structure of T-cell surface glycoprotein CD1d antigen.[1] | |||||||||
Identifiers | |||||||||
Symbol | C1-set | ||||||||
Pfam | PF07654 | ||||||||
InterPro | IPR003597 | ||||||||
|
C1-set domains are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules,[2][3] and in various T-cell receptors.
Human proteins containing this domain
AZGP1; B2M; CD1A; CD1B; CD1C; CD1D; CD1E; DMA; DQB2; DRB1; ELK2P1; FCGRT; HFE; HHLA2; HLA-A; HLA-B; HLA-B35; HLA-B57; HLA-C; HLA-CW; HLA-Cw; HLA-D; HLA-DMA; HLA-DMB; HLA-DOA; HLA-DOB; HLA-DP; HLA-DPA1; HLA-DPB1; HLA-DQA1; HLA-DQA2; HLA-DQB1; HLA-DQB2; HLA-DRA; HLA-DRB1; HLA-DRB2; HLA-DRB3; HLA-DRB4; HLA-DRw12; HLA-Dw12; HLA-E; HLA-F; HLA-G; HLA-G2.2; HLA-H; HLAC; IGHA1; IGHA2; IGHD; IGHE; IGHG1; IGHG2; IGHG3; IGHG4; IGHM; IGHV4-31; IGKC; IGKV1-5; IGKV2-24; IGL@; IGLC1; IGLC3; IGLL1; IGLV2-14; IGLV3-21; IGLV3-25; IGLV4-3; MICA; MICB; MR1; SIRPA; SIRPB1; SIRPG; SNC73; TAPBP; TAPBPL; TRBC1; TRBV19; TRBV21-1; TRBV3-1; TRBV5-4; TRBV7-2; micB;
References
- ^ Zajonc DM, Cantu C, Mattner J, et al. (August 2005). "Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor". Nat. Immunol. 6 (8): 810–8. doi:10.1038/ni1224. PMC 2045075. PMID 16007091.
- ^ Cresswell P, Pamer E (1998). "Mechanisms of MHC class I--restricted antigen processing". Annu. Rev. Immunol. 16 (1): 323–358. doi:10.1146/annurev.immunol.16.1.323. PMID 9597133.
- ^ Ono SJ, Radosevich M (2003). "Novel mechanisms of class II major histocompatibility complex gene regulation". Immunol Res. 27 (1): 85–106. doi:10.1385/IR:27:1:85. PMID 12637770.
![]() | This membrane protein–related article is a stub. You can help Wikipedia by expanding it. |
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 C1-set domain Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Adhes-Ig_like C2-set_2 I-set ig Ig_2 Ig_3 Marek_A PTCRA V-set |
Similarity to PfamA using HHSearch: | ig I-set C2-set_2 Ig_2 Ig_3 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003597
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 C1-set domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules [PUBMED:9597133, PUBMED:12637770], and in various T-cell receptors.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
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 32 members:
Adeno_E3_CR1 Adhes-Ig_like 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_CD47Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (71) |
Full (16226) |
Representative proteomes | UniProt (53423) |
NCBI (78994) |
Meta (0) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (871) |
RP35 (3428) |
RP55 (9570) |
RP75 (15971) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (71) |
Full (16226) |
Representative proteomes | UniProt (53423) |
NCBI (78994) |
Meta (0) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (871) |
RP35 (3428) |
RP55 (9570) |
RP75 (15971) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Bateman A |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 71 |
Number in full: | 16226 |
Average length of the domain: | 82.20 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 31.68 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 86 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Interactions
There are 38 interactions for this family. More...
Stap_Strp_toxin Cytomega_US3 Hemagglutinin Bet_v_1 Arena_glycoprot Pox_T4_N MHC_I MHC_II_beta Adeno_GP19K DUF1968 MHC_II_alpha Stap_Strp_tox_C Ig_3 MHC_I Herpes_gE Ig_2 PRY Hemagglutinin Cytomega_US3 MHC_II_beta SPRY Ig_2 Pox_T4_C Stap_Strp_toxin DUF1968 MA-Mit SSL_OB MHC_II_alpha Lectin_C Lectin_C SVA C1-set ig Stap_Strp_tox_C IgG_binding_B B V-set V-setStructures
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 C1-set domain has been found. There are 6266 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.
Loading structure mapping...