Summary: CD47 immunoglobulin-like domain
CD47 immunoglobulin-like domain Provide feedback
This family represents the CD47 leukocyte antigen V-set like Ig domain [1,2].
Koshimizu H, Araki T, Takai S, Yokomaku D, Ishikawa Y, Kubota M, Sano S, Hatanaka H, Yamada M; , J Neurochem 2002;82:249-257.: Expression of CD47/integrin-associated protein induces death of cultured cerebral cortical neurons. PUBMED:12124426 EPMC:12124426
Lindberg FP, Gresham HD, Reinhold MI, Brown EJ; , J Cell Biol 1996;134:1313-1322.: Integrin-associated protein immunoglobulin domain is necessary for efficient vitronectin bead binding. PUBMED:8794870 EPMC:8794870
Internal database links
|SCOOP:||C2-set_2 Receptor_2B4 Ig_2 Ig_3 Ig_4 Ig_5 Izumo-Ig UL141|
|Similarity to PfamA using HHSearch:||ig C1-set I-set V-set Ig_4|
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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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 . 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 . 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 28 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_4 Ig_5 Ig_Tie2_1 Izumo-Ig K1 Lep_receptor_Ig Marek_A PTCRA Receptor_2B4 SVA UL141 V-set V-set_2 V-set_CD47
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pfam-B_2739 (release 7.5)|
|Author:||Mifsud W, Bateman A|
|Number in seed:||12|
|Number in full:||163|
|Average length of the domain:||121.70 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||41.67 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 V-set_CD47 domain has been found. There are 11 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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