Summary: Scavenger receptor cysteine-rich domain
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This is the Wikipedia entry entitled "Scavenger receptor cysteine-rich protein domain". More...
Scavenger receptor cysteine-rich protein domain Edit Wikipedia article
SRCR | |||||||||
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![]() structure of m2bp scavenger receptor cysteine-rich domain
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Identifiers | |||||||||
Symbol | SRCR | ||||||||
Pfam | PF00530 | ||||||||
InterPro | IPR001190 | ||||||||
PROSITE | PDOC00348 | ||||||||
SCOP | 1by2 | ||||||||
SUPERFAMILY | 1by2 | ||||||||
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In molecular biology, the protein domain SRCR is short for Scavenger receptor cysteine-rich domain. They are found solely in eukaryotes. These domains are present on the cell membrane and have a role in binding to specific ligands and are often found to be involved with the immune system.[1]
Contents
Function
The function of these endocytic receptors are to mediating non-opsonic phagocytosis in response to foreign ligands. This triggers various processes of host defence and immune response.[2]
Structure
The structure contains a six stranded beta-sheet and one alpha-helix.[1]
Examples
The speract receptor found in egg, is a transmembrane glycoprotein.[3] Other members of this family include the macrophage scavenger receptor type I, an enteropeptidase, and T-cell surface glycoprotein CD5.
References
- ^ a b Hohenester E; Sasaki T; Timpl R (1999). "Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily.". Nat Struct Biol. 6 (3): 228–32. PMID 10074941. doi:10.1038/6669.
- ^ Liu L, Yang J, Qiu L, Wang L, Zhang H, Wang M, et al. (2011). "A novel scavenger receptor-cysteine-rich (SRCR) domain containing scavenger receptor identified from mollusk mediated PAMP recognition and binding.". Dev Comp Immunol. 35 (2): 227–39. PMID 20888856. doi:10.1016/j.dci.2010.09.010.
- ^ Resnick D; Pearson A; Krieger M (January 1994). "The SRCR superfamily: a family reminiscent of the Ig superfamily". Trends Biochem. Sci. 19 (1): 5–8. PMID 8140623. doi:10.1016/0968-0004(94)90165-1.
This article incorporates text from the public domain Pfam and InterPro IPR001190
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.
Scavenger receptor cysteine-rich domain Provide feedback
These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Literature references
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Resnick D, Pearson A, Krieger M; , Trends Biochem Sci 1994;19:5-8.: The SRCR superfamily - A family reminiscent of the Ig superfamily. PUBMED:8140623 EPMC:8140623
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Hohenester E, Sasaki T, Timpl R; , Nat Struct Biol 1999;6:228-232.: Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily. PUBMED:10074941 EPMC:10074941
Internal database links
SCOOP: | Hepsin-SRCR SRCR_2 |
Similarity to PfamA using HHSearch: | Hepsin-SRCR SRCR_2 |
External database links
PROSITE: | PDOC00348 |
SCOP: | 1by2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001190
The scavenger receptor cysteine-rich (SRCR) domain is an ancient and highly conserved domain of about 110 residues which is found in diverse secreted and cell-surface proteins, like the type I scavenger receptor, the speract receptor, CD5/Ly-1, CD6, or complement factor I [PUBMED:1978939]. Tandem repeats of SRCR domains are common in the membrane bound proteins. Most SRCR domains have six to eight cysteines that participate in intradomain disulfide bonds. SRCR domains have been subdivided into two groups, A and B, primarily on the differences in the spacing pattern between the cysteine residues [PUBMED:8140623, PUBMED:10074941].
Although the biochemical functions of SRCR domains have not been established with certainty, they are likely to mediate protein-protein interactions and ligand binding [PUBMED:8140623, PUBMED:10074941].
Determination of the crystal structure of the SRCR domain of M2BP reveals that the M2NP SRCR adopts a compact fold of approximate dimensions 22 x 26 x 30 Angstrom, organised around a curved six-stranded beta-sheet cradling an alpha- helix [PUBMED:10074941].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
Molecular function | scavenger receptor activity (GO:0005044) |
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 SRCR (CL0550), which has the following description:
The clan contains the following 3 members:
Hepsin-SRCR SRCR SRCR_2Alignments
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...
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 (77) |
Full (25439) |
Representative proteomes | UniProt (36356) |
NCBI (71939) |
Meta (21) |
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RP15 (6782) |
RP35 (10856) |
RP55 (18470) |
RP75 (26262) |
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HTML | |||||||||
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 (77) |
Full (25439) |
Representative proteomes | UniProt (36356) |
NCBI (71939) |
Meta (21) |
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RP15 (6782) |
RP35 (10856) |
RP55 (18470) |
RP75 (26262) |
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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: | Reference [1] |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 77 |
Number in full: | 25439 |
Average length of the domain: | 96.50 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 42.70 % |
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: | 100 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 SRCR domain has been found. There are 27 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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