Summary: C1q domain
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C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Internal database links
SCOOP: | BclA_C PA14 TNF |
Similarity to PfamA using HHSearch: | TNF BclA_C |
External database links
PROSITE: | PDOC00857 |
SCOP: | 1c28 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001073
This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain [PUBMED:1706597]. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [PUBMED:2591537, PUBMED:2019595]. This domain is also found in multimerin and EMILIN proteins.
The C-terminal globular domain of the C1q subcomponents and collagen types VIII and X is important both for the correct folding and alignment of the triple helix and for protein-protein recognition events [PUBMED:1867713]. For collagen type X it has been suggested that the domain is important for initiation and maintenance of the correct assembly of the protein [PUBMED:1860888]. The globular head is a trimer of C1q domains. Each individual C1q adopts a 10-strand Jelly-roll fold arranged in two antiparallel 5-stranded beta-sheets [PUBMED:22892318]. There are two well conserved regions within the C1q domain: an aromatic motif is located within the first half of the domain, the other conserved region is located near the C-terminal extremity.
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 C1q_TNF (CL0100), which has the following description:
The members of the C1q and TNF superfamily are involved in a diverse set of functions, which include: defense, inflammation, apoptosis, autoimmunity differentiation, organogenesis, hibernation and insulin-resistant obesity [1]. Both C1q and TNF domains form a compact jelly-roll beta- sandwich. The core of these structures are conserved between the two families and corresponds to the detectable sequence similarity. Proteins containing both of these domains, form trimers before they are active. However, the surfaces of the domains are quite different and this difference is thought to give rise to the function difference between the clan members[1].
The clan contains the following 7 members:
BclA_C C1q Chlam_vir DUF1860 DUF3845 Phage_tail_NK TNFAlignments
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...
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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 (32) |
Full (8019) |
Representative proteomes | UniProt (14136) |
NCBI (21088) |
Meta (343) |
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RP15 (1286) |
RP35 (2545) |
RP55 (5595) |
RP75 (8372) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (32) |
Full (8019) |
Representative proteomes | UniProt (14136) |
NCBI (21088) |
Meta (343) |
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RP15 (1286) |
RP35 (2545) |
RP55 (5595) |
RP75 (8372) |
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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: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 32 |
Number in full: | 8019 |
Average length of the domain: | 123.70 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 33.04 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 127 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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...
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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 C1q domain has been found. There are 111 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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