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47  structures 315  species 1  interaction 2356  sequences 38  architectures

Family: C1q (PF00386)

Summary: C1q domain

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This is the Wikipedia entry entitled "C1q domain". More...

C1q domain Edit Wikipedia article

C1q domain
PDB 1o91 EBI.jpg
crystal structure of a collagen viii nc1 domain trimer
Identifiers
Symbol C1q
Pfam PF00386
Pfam clan CL0100
InterPro IPR001073
PROSITE PDOC00857
SCOP 1c28
SUPERFAMILY 1c28

In molecular biology, the C1q domain is a conserved protein domain. 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.[1] The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X.[2][3]

References[edit]

  1. ^ Sellar GC, Blake DJ, Reid KB (March 1991). "Characterization and organization of the genes encoding the A-, B- and C-chains of human complement subcomponent C1q. The complete derived amino acid sequence of human C1q". Biochem. J. 274 (2): 481–90. PMC 1150164. PMID 1706597. 
  2. ^ Petry F, Reid KB, Loos M (November 1989). "Molecular cloning and characterization of the complementary DNA coding for the B-chain of murine Clq". FEBS Lett. 258 (1): 89–93. doi:10.1016/0014-5793(89)81622-9. PMID 2591537. 
  3. ^ Muragaki Y, Jacenko O, Apte S, Mattei MG, Ninomiya Y, Olsen BR (April 1991). "The alpha 2(VIII) collagen gene. A novel member of the short chain collagen family located on the human chromosome 1". J. Biol. Chem. 266 (12): 7721–7. PMID 2019595. 

This article incorporates text from the public domain Pfam and InterPro IPR001073

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.

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C1q is a subunit of the C1 enzyme complex that activates the serum complement system.

Internal database links

External database links

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.

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 2 members:

C1q TNF

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
(46)
Full
(2356)
Representative proteomes NCBI
(1977)
Meta
(431)
RP15
(266)
RP35
(375)
RP55
(622)
RP75
(1129)
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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
(46)
Full
(2356)
Representative proteomes NCBI
(1977)
Meta
(431)
RP15
(266)
RP35
(375)
RP55
(622)
RP75
(1129)
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
(46)
Full
(2356)
Representative proteomes NCBI
(1977)
Meta
(431)
RP15
(266)
RP35
(375)
RP55
(622)
RP75
(1129)
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.

Pfam alignments:

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: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 46
Number in full: 2356
Average length of the domain: 122.60 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 35.37 %

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 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 127
Family (HMM) version: 16
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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Interactions

There is 1 interaction for this family. More...

C1q

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 47 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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