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706  structures 513  species 0  interactions 100725  sequences 2014  architectures

Family: Sushi (PF00084)

Summary: Sushi repeat (SCR repeat)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Sushi domain Edit Wikipedia article

Sushi domain (SCR/CCP)
Identifiers
SymbolSushi
PfamPF00084
InterProIPR000436
CATH1g4g
SCOPe1hfi / SUPFAM
CDDcd00033

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:

References

  1. ^ 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.
  2. ^ Lomas-Francis, Christine; Reid, Marion E. (2004). The blood group antigen: factsbook. Boston: Academic Press. ISBN 0-12-586585-6.
This article incorporates text from the public domain Pfam and InterPro: IPR000436

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

  1. Ichinose A, Bottenus RE, Davie EW; , J Biol Chem 1990;265:13411-13414.: Structure of transglutaminases. PUBMED:1974250 EPMC:1974250

  2. 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

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_like

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...

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)
RP15
(12945)
RP35
(32157)
RP55
(85496)
RP75
(115859)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(33)
Full
(100725)
Representative proteomes UniProt
(169167)
RP15
(12945)
RP35
(32157)
RP55
(85496)
RP75
(115859)
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
(33)
Full
(100725)
Representative proteomes UniProt
(169167)
RP15
(12945)
RP35
(32157)
RP55
(85496)
RP75
(115859)
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: Swissprot_feature_table
Previous IDs: sushi;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
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 View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 17.0
Trusted cut-off 20.7 17.0
Noise cut-off 20.6 16.9
Model length: 56
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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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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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
A0A0G2JTG3 View 3D Structure Click here
A0A0G2JTG3 View 3D Structure Click here
A0A0G2JYC4 View 3D Structure Click here
A0A0G2JYC4 View 3D Structure Click here
A0A0G2JYC4 View 3D Structure Click here
A0A0G2JYC4 View 3D Structure Click here
A0A0G2K0Q8 View 3D Structure Click here
A0A0G2K684 View 3D Structure Click here
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A0A0G2K7X7 View 3D Structure Click here
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A0A0G2K975 View 3D Structure Click here
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A0A0G2KVK9 View 3D Structure Click here
A0A0G2KVK9 View 3D Structure Click here
A0A0G2LAP2 View 3D Structure Click here
A0A0G2QC50 View 3D Structure Click here
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A0A0R4IAG9 View 3D Structure Click here
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A0A0R4IC53 View 3D Structure Click here
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A0A0R4IC53 View 3D Structure Click here
A0A0R4IIJ1 View 3D Structure Click here
A0A0R4IIN5 View 3D Structure Click here
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A0A0R4IJM1 View 3D Structure Click here
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A0A0R4IJM1 View 3D Structure Click here
A0A0R4IJM1 View 3D Structure Click here
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A0A0R4IL35 View 3D Structure Click here
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A0A0R4IPL8 View 3D Structure Click here
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A0A0R4IPP5 View 3D Structure Click here
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A0A0R4IXT8 View 3D Structure Click here
A0A1N7SYP5 View 3D Structure Click here
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A0A2R8Q0J7 View 3D Structure Click here
A0A2R8Q0J7 View 3D Structure Click here
A0A2R8Q3K1 View 3D Structure Click here
A0A2R8Q401 View 3D Structure Click here
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A0A2R8Q401 View 3D Structure Click here
A0A2R8QGZ8 View 3D Structure Click here
A0A2R8QK78 View 3D Structure Click here
A0A2R8QKR9 View 3D Structure Click here
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A0A2R8QMP2 View 3D Structure Click here
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A0A2R8QMP2 View 3D Structure Click here
A0A2R8QMP2 View 3D Structure Click here
A0A2R8QNI9 View 3D Structure Click here
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A0A668KLU9 View 3D Structure Click here
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A1Z8V0 View 3D Structure Click here
A2AR64 View 3D Structure Click here
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A2BFS8 View 3D Structure Click here
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A4IG76 View 3D Structure Click here
A8JUX3 View 3D Structure Click here
A8JUX3 View 3D Structure Click here
A8JUX3 View 3D Structure Click here
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B1H260 View 3D Structure Click here
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B5DEH7 View 3D Structure Click here
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B5DF94 View 3D Structure Click here
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D3Z8I2 View 3D Structure Click here
D3ZSY7 View 3D Structure Click here
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D4A231 View 3D Structure Click here
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E7F463 View 3D Structure Click here
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E7F8X0 View 3D Structure Click here
E7F8X0 View 3D Structure Click here
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E7F9K6 View 3D Structure Click here
E7FBP0 View 3D Structure Click here
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E7FCC2 View 3D Structure Click here
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E7FFU9 View 3D Structure Click here
E9Q3H4 View 3D Structure Click here
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F1LXT9 View 3D Structure Click here
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F1MA42 View 3D Structure Click here
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F1QAJ3 View 3D Structure Click here
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F1QE83 View 3D Structure Click here
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F1QEZ8 View 3D Structure Click here
F1QF24 View 3D Structure Click here
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F1QHZ0 View 3D Structure Click here
F1QIT5 View 3D Structure Click here
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F1QJB3 View 3D Structure Click here
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F1QX38 View 3D Structure Click here
F1R886 View 3D Structure Click here
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F1RDY7 View 3D Structure Click here
F8W252 View 3D Structure Click here
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M0R5N9 View 3D Structure Click here
O00187 View 3D Structure Click here
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O14594 View 3D Structure Click here
O60687 View 3D Structure Click here
O60687 View 3D Structure Click here
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O88174 View 3D Structure Click here
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P00736 View 3D Structure Click here
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P00751 View 3D Structure Click here
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P01589 View 3D Structure Click here
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P02749 View 3D Structure Click here
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P04186 View 3D Structure Click here
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P05160 View 3D Structure Click here
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