Summary: Sushi repeat (SCR repeat)
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Sushi domain Edit Wikipedia article
| Sushi domain (SCR/CCP) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||||
| Symbol | Sushi | ||||||||||
| Pfam | PF00084 | ||||||||||
| InterPro | IPR000436 | ||||||||||
| CATH | 1g4g | ||||||||||
| SCOPe | 1hfi / SUPFAM | ||||||||||
| CDD | cd00033 | ||||||||||
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Sushi domain is an evolutionarily conserved protein domain. It is also known as Complement control protein (CCP) modules or short consensus repeats (SCR).
Sushi domains exist in a wide variety of complement and adhesion proteins. The structure is known for this domain; it is based on a beta-sandwich arrangement - one face made up of three β-strands hydrogen-bonded to form a triple-stranded region at its centre, and the other face formed from two separate β-strands.[1]
CD21 (also called C3d receptor, CR2, Epstein Barr virus receptor or EBV-R) is the receptor for EBV and for C3d, C3dg and iC3b. Complement components may activate B cells through CD21. CD21 is part of a large signal-transduction complex that also involves CD19, CD81, and Leu13.
Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins.[2] Complement decay-accelerating factor (Antigen CD55) belongs to the Cromer blood group system and is associated with Cr(a), Dr(a), Es(a), Tc(a/b/c), Wd(a), WES(a/b), IFC and UMC antigens. Complement receptor type 1 (C3b/C4b receptor) (Antigen CD35) belongs to the Knops blood group system and is associated with Kn(a/b), McC(a), Sl(a) and Yk(a) antigens.
Subfamilies
Examples
Human genes encoding proteins containing this domain include:
- AGC1, APOH,
- BCAN, BF,
- C1R, C1S, C2, C4BPA, C4BPB, C6, C7, CD46, CD55, CFB, CFH, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CR1, CR1L, CR2, CSMD1, CSMD2, CSMD3, CSPG3,
- DAF,
- F13B, FHR4, GABBR1,
- HP,
- IL2RA,
- KIAA0247,
- MASP1, MASP2,
- PAPPA, PAPPA2, psk-3,
- RAMP,
- SEL-OB, SELE, SELL, SELP, SEZ6, SEZ6L, SEZ6L2, SNED1, SRPX, SRPX2, SUSD1, SUSD2, SUSD4, SVEP1, SEZ6L2,
- TAOK1, TPO, VCAN
References
- ^ Campbell ID, Baron M, Day AJ, Sim RB, Norman DG, Barlow PN (1991). "Three-dimensional structure of a complement control protein module in solution". J. Mol. Biol. 219 (4): 717–725. doi:10.1016/0022-2836(91)90666-T. PMID 1829116.
- ^ Lomas-Francis, Christine; Reid, Marion E. (2004). The blood group antigen: factsbook. Boston: Academic Press. ISBN 0-12-586585-6.
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.
Sushi repeat (SCR repeat) Provide feedback
No Pfam abstract.
Literature references
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Ichinose A, Bottenus RE, Davie EW; , J Biol Chem 1990;265:13411-13414.: Structure of transglutaminases. PUBMED:1974250 EPMC:1974250
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Kato H, Enjyoji K; , Biochemistry 1991;30:11687-11694.: Amino acid sequence and location of the disulfide bonds in bovine beta 2 glycoprotein I: the presence of five Sushi domains. PUBMED:1751487 EPMC:1751487
External database links
| HOMSTRAD: | ccH |
| SCOP: | 1hfi |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000436
The extracellular sushi domain is characterised by a consensus sequence spanning ~60 residues containing four invariant cysteine residues forming two disulfide-bridges (I-III and II-IV), a highly conserved tryptophan, and conserved glycine, proline, and hydrophobic residues [ PUBMED:2751824 ]. Sushi domains are known to be involved in many recognition processes, including the binding of several complement factors to fragments C3b and C4b [ PUBMED:2751824 ]. The sushi domain is also known as the complement controle protein (CCP) module or the short consensus repeat (SCR).
Several structure of the sushi domain have been solved (see for example {PDB:1HCC}) [ PUBMED:1829116 ]. The sushi domain folds into a small and compact hydrophobic core enveloped by six beta-strands and stabilised by two disulfide bridges. The relative structural orientation of the Beta-2 and Beta-4 strands is shared by all the sushi structures, whereas the topology of the other strands relative to this central conserved core is variable, especially at the regions that form the interfaces with the preceding and following domains [ PUBMED:10775260 ].
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 EGF (CL0001), which has the following description:
Members of this clan all belong to the EGF superfamily. This particular superfamily is characterised as having least 6 cysteine residues. These cysteines form disulphide bonds, in the order 1-3, 2-4, 5-6, which are essential for the stability of the EGF fold. These disulphide bonds are stacked in a ladder-like arrangement. The Laminin EGF family is distinguished by having an an additional disulphide bond. The function of the domains within this family remains unclear, but they are thought to largely perform a structural role. More often than not, these domains are arranged in tandem repeats in extracellular proteins.
The clan contains the following 22 members:
cEGF CFC DSL EGF EGF_2 EGF_3 EGF_alliinase EGF_CA EGF_MSP1_1 EGF_Tenascin Ephrin_rec_like Fibrillin_U_N FOLN FXa_inhibition Gla hEGF I-EGF_1 Laminin_EGF Plasmod_Pvs28 Sushi Sushi_2 Tme5_EGF_likeAlignments
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...
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 (33) |
Full (100725) |
Representative proteomes | UniProt (169167) |
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|---|---|---|---|---|---|---|---|
| RP15 (12945) |
RP35 (32157) |
RP55 (85496) |
RP75 (115859) |
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| Jalview | |||||||
| HTML | |||||||
| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (33) |
Full (100725) |
Representative proteomes | UniProt (169167) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (12945) |
RP35 (32157) |
RP55 (85496) |
RP75 (115859) |
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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: | Swissprot_feature_table |
| Previous IDs: | sushi; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Sonnhammer ELL 
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| Number in seed: | 33 |
| Number in full: | 100725 |
| Average length of the domain: | 56.80 aa |
| Average identity of full alignment: | 27 % |
| Average coverage of the sequence by the domain: | 30.78 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 56 | ||||||||||||
| Family (HMM) version: | 22 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Viruses
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Viroids
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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 Sushi domain has been found. There are 706 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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