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335  structures 499  species 0  interactions 16908  sequences 1108  architectures

Family: Fibrinogen_C (PF00147)

Summary: Fibrinogen beta and gamma chains, C-terminal globular domain

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This is the Wikipedia entry entitled "Fibrinogen". More...

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Fibrinogen beta and gamma chains, C-terminal globular domain Provide feedback

No Pfam abstract.

Literature references

  1. Spraggon G, Everse SJ, Doolittle RF , Nature 1997;389:455-462.: Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin. PUBMED:9333233 EPMC:9333233


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002181

Fibrinogen plays key roles in both blood clotting and platelet aggregation. During blood clot formation, the conversion of soluble fibrinogen to insoluble fibrin is triggered by thrombin, resulting in the polymerisation of fibrin, which forms a soft clot; this is then converted to a hard clot by factor XIIIA, which cross-links fibrin molecules. Platelet aggregation involves the binding of the platelet protein receptor integrin alpha(IIb)-beta(3) to the C-terminal D domain of fibrinogen [ PUBMED:12799374 ]. In addition to platelet aggregation, platelet-fibrinogen interaction mediates both adhesion and fibrin clot retraction.

Fibrinogen occurs as a dimer, where each monomer is composed of three non-identical chains, alpha, beta and gamma, linked together by several disulphide bonds [ PUBMED:11460466 ]. The N-terminals of all six chains come together to form the centre of the molecule (E domain), from which the monomers extend in opposite directions as coiled coils, followed by C-terminal globular domains (D domains). Therefore, the domain composition is: D-coil-E-coil-D. At each end, the C-terminal of the alpha chain extends beyond the D domain as a protuberance that is important for cross-linking the molecule.

During clot formation, the N-terminal fragments of the alpha and beta chains (within the E domain) in fibrinogen are cleaved by thrombin, releasing fibrinopeptides A and B, respectively, and producing fibrin. This cleavage results in the exposure of four binding sites on the E domain, each of which can bind to a D domain from different fibrin molecules. The binding of fibrin molecules produces a polymer consisting of a lattice network of fibrins that form a long, branching, flexible fibre [ PUBMED:11593005 , PUBMED:15837518 ]. Fibrin fibres interact with platelets to increase the size of the clot, as well as with several different proteins and cells, thereby promoting the inflammatory response and concentrating the cells required for wound repair at the site of damage.

This entry represents the C-terminal globular D domain of the alpha, beta and gamma chains. These domains are related to domains in other proteins: in the Parastichopus parvimensis (Sea cucumber) fibrogen-like FreP-A and FreP-B proteins; in the C terminus of the Drosophila scabrous protein that is involved in the regulation of neurogenesis, possibly through the inhibition of R8 cell differentiation; and in ficolin proteins, which display lectin activity towards N-acetylglucosamine through their fibrogen-like domains [ PUBMED:12396010 ].

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 Fibrinogen_C (CL0422), which has the following description:

This is a collection of families with C-terminal domains that are of similar structure.

The clan contains the following 2 members:

COLFI Fibrinogen_C

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
(5)
Full
(16908)
Representative proteomes UniProt
(30440)
RP15
(4744)
RP35
(7732)
RP55
(13763)
RP75
(17586)
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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
(5)
Full
(16908)
Representative proteomes UniProt
(30440)
RP15
(4744)
RP35
(7732)
RP55
(13763)
RP75
(17586)
Alignment:
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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
(5)
Full
(16908)
Representative proteomes UniProt
(30440)
RP15
(4744)
RP35
(7732)
RP55
(13763)
RP75
(17586)
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: Prosite
Previous IDs: fibrinogen_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
Number in seed: 5
Number in full: 16908
Average length of the domain: 191.1 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 34.2 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 221
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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 Fibrinogen_C domain has been found. There are 335 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
A0A044R241 View 3D Structure Click here
A0A044S8H6 View 3D Structure Click here
A0A077Z6R9 View 3D Structure Click here
A0A077ZBV5 View 3D Structure Click here
A0A077ZIS9 View 3D Structure Click here
A0A0B4K7T3 View 3D Structure Click here
A0A0G2K1L0 View 3D Structure Click here
A0A0G2K603 View 3D Structure Click here
A0A0K0DTY0 View 3D Structure Click here
A0A0K0E646 View 3D Structure Click here
A0A0K0EL82 View 3D Structure Click here
A0A0K0EQH0 View 3D Structure Click here
A0A0N4UEB7 View 3D Structure Click here
A0A0N4UJJ2 View 3D Structure Click here
A0A0R4IQ22 View 3D Structure Click here
A0A0R4ISF8 View 3D Structure Click here
A0A0R4IXV0 View 3D Structure Click here
A0A140LG86 View 3D Structure Click here
A0A2R8PY83 View 3D Structure Click here
A0A2R8PYX8 View 3D Structure Click here
A0A2R8Q779 View 3D Structure Click here
A0A2R8Q9F1 View 3D Structure Click here
A0A2R8QBE6 View 3D Structure Click here
A0A2R8QL80 View 3D Structure Click here
A0A2R8QRA8 View 3D Structure Click here
A0A2R8RUH9 View 3D Structure Click here
A0A3P7F3B5 View 3D Structure Click here
A0A3P7FTU8 View 3D Structure Click here
A0A3P7G996 View 3D Structure Click here
A0A3P7PUY4 View 3D Structure Click here
A0A8J8 View 3D Structure Click here
A1Z7G6 View 3D Structure Click here
A2AV25 View 3D Structure Click here
A2CF37 View 3D Structure Click here
B0UX68 View 3D Structure Click here
B0UXH5 View 3D Structure Click here
B2RYM1 View 3D Structure Click here
B7Z0B2 View 3D Structure Click here
B8A5L6 View 3D Structure Click here
C1IHU8 View 3D Structure Click here