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6803  structures 252  species 0  interactions 20971  sequences 264  architectures

Family: C1-set (PF07654)

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
PDB 1z5l EBI.jpg
Structure of T-cell surface glycoprotein CD1d antigen.[1]
Identifiers
SymbolC1-set
PfamPF07654
InterProIPR003597

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

  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

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

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 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
(70)
Full
(20971)
Representative proteomes UniProt
(67008)
RP15
(1193)
RP35
(5284)
RP55
(16788)
RP75
(22469)
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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
(70)
Full
(20971)
Representative proteomes UniProt
(67008)
RP15
(1193)
RP35
(5284)
RP55
(16788)
RP75
(22469)
Alignment:
Format:
Order:
Sequence:
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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
(70)
Full
(20971)
Representative proteomes UniProt
(67008)
RP15
(1193)
RP35
(5284)
RP55
(16788)
RP75
(22469)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: 70
Number in full: 20971
Average length of the domain: 82.30 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 32.53 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 86
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 C1-set domain has been found. There are 6803 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
A0A023IKK2 View 3D Structure Click here
A0A0A6YXN8 View 3D Structure Click here
A0A0A6YXN8 View 3D Structure Click here
A0A0A6YYP6 View 3D Structure Click here
A0A0A6YYP6 View 3D Structure Click here
A0A0G2JMH6 View 3D Structure Click here
A0A0G2JTD2 View 3D Structure Click here
A0A0G2JTD2 View 3D Structure Click here
A0A0G2JTD2 View 3D Structure Click here
A0A0G2K0R1 View 3D Structure Click here
A0A0G2K1E1 View 3D Structure Click here
A0A0G2K7V7 View 3D Structure Click here
A0A0G2K8A4 View 3D Structure Click here
A0A0G2K8K8 View 3D Structure Click here
A0A0G2K8N2 View 3D Structure Click here
A0A0G2K8R6 View 3D Structure Click here
A0A0G2KIH5 View 3D Structure Click here
A0A0G2KL77 View 3D Structure Click here
A0A0G2L594 View 3D Structure Click here
A0A0N4SU34 View 3D Structure Click here
A0A0R4IK44 View 3D Structure Click here
A0A0R4IR31 View 3D Structure Click here
A0A0R4IRA8 View 3D Structure Click here
A0A0R4ISW2 View 3D Structure Click here
A0A0R4IW73 View 3D Structure Click here
A0A0R4IW73 View 3D Structure Click here
A0A0R4IW73 View 3D Structure Click here
A0A0R4IWN3 View 3D Structure Click here
A0A0R4IZK4 View 3D Structure Click here
A0A1L1QZR0 View 3D Structure Click here
A0A2R8PYQ6 View 3D Structure Click here
A0A2R8Q639 View 3D Structure Click here
A0A2R8Q771 View 3D Structure Click here
A0A2R8QFS1 View 3D Structure Click here
A0A2R8QHV2 View 3D Structure Click here
A0A2R8QQR6 View 3D Structure Click here
A0A2R8QSS1 View 3D Structure Click here
A0A2R8RPU4 View 3D Structure Click here
A0A494BB12 View 3D Structure Click here
A0A5B9 View 3D Structure Click here
A0M8Q6 View 3D Structure Click here
A4FUM4 View 3D Structure Click here
A7VMS2 View 3D Structure Click here
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B7Z8K6 View 3D Structure Click here
B8JM90 View 3D Structure Click here
B9A064 View 3D Structure Click here
D3ZKH0 View 3D Structure Click here
D4A0E0 View 3D Structure Click here
D4A6L1 View 3D Structure Click here
E7F146 View 3D Structure Click here
E7F1G6 View 3D Structure Click here
E7F1M4 View 3D Structure Click here
E7F3P0 View 3D Structure Click here
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E7FAH6 View 3D Structure Click here
E7FE17 View 3D Structure Click here
E9PTZ9 View 3D Structure Click here
E9QCH2 View 3D Structure Click here
F1LPW0 View 3D Structure Click here
F1LPW0 View 3D Structure Click here
F1LPW0 View 3D Structure Click here
F1LPW0 View 3D Structure Click here
F1LQF2 View 3D Structure Click here
F1LSU0 View 3D Structure Click here
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F1M520 View 3D Structure Click here
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F1MAM7 View 3D Structure Click here
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F1MAR7 View 3D Structure Click here
F1Q8N9 View 3D Structure Click here
F1Q8P0 View 3D Structure Click here
F1QAA3 View 3D Structure Click here
F1QKH0 View 3D Structure Click here
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F1QNN0 View 3D Structure Click here
F1QUL1 View 3D Structure Click here
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F6NRL9 View 3D Structure Click here
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F7CXU4 View 3D Structure Click here
F7EWE4 View 3D Structure Click here
F7FN89 View 3D Structure Click here
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G3UXE9 View 3D Structure Click here
G3V627 View 3D Structure Click here
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L7N479 View 3D Structure Click here
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O00241 View 3D Structure Click here
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O15533 View 3D Structure Click here
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P0CF51 View 3D Structure Click here
P0CF74 View 3D Structure Click here
P0CG04 View 3D Structure Click here
P0DOY2 View 3D Structure Click here
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P10321 View 3D Structure Click here
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Q95574 View 3D Structure Click here
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Q95II0 View 3D Structure Click here
Q99JC6 View 3D Structure Click here
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Q9W257 View 3D Structure Click here
U6BNE9 View 3D Structure Click here
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