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2328  structures 510  species 15  interactions 16594  sequences 70  architectures

Family: C1-set (PF07654)

Summary: Immunoglobulin C1-set domain

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This is the Wikipedia entry entitled "Immunoglobulin C1-set domain". More...

Immunoglobulin C1-set domain Edit Wikipedia article

Immunoglobulin C1-set domain
PDB 1z5l EBI.jpg
Structure of T-cell surface glycoprotein CD1d antigen.[1]
Identifiers
Symbol C1-set
Pfam PF07654
InterPro IPR003597
OPM protein 1z5l

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[edit]

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[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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 article incorporates text from the public domain Pfam and InterPro IPR003597

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No Pfam abstract.

Internal database links

External database links

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...

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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 24 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_Tie2_1 IZUMO K1 Lep_receptor_Ig Marek_A PTCRA Receptor_2B4 SVA V-set 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(128)
Full
(16594)
Representative proteomes NCBI
(24856)
Meta
(1)
RP15
(174)
RP35
(356)
RP55
(861)
RP75
(2190)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(128)
Full
(16594)
Representative proteomes NCBI
(24856)
Meta
(1)
RP15
(174)
RP35
(356)
RP55
(861)
RP75
(2190)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(128)
Full
(16594)
Representative proteomes NCBI
(24856)
Meta
(1)
RP15
(174)
RP35
(356)
RP55
(861)
RP75
(2190)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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
Author: Bateman A
Number in seed: 128
Number in full: 16594
Average length of the domain: 82.80 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 31.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 83
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 15 interactions for this family. More...

MHC_I MHC_II_beta VWA IgG_binding_B C1-set Stap_Strp_tox_C V-set DUF1968 Stap_Strp_toxin Tissue_fac MHC_II_alpha B Lectin_C DUF1954 ig

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 C1-set domain has been found. There are 2328 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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