Summary: Cell surface antigen I/II C2 terminal domain
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Cell surface antigen I/II C2 terminal domain Provide feedback
This is the second domain (C2) located in the C-terminal region found in antigen I/II type adhesin protein AspA from S. pyogenes. Together with C3, these two domains form an elongated structure, each domain adopts the DEv-IgG fold. Similar to the classical IgG folds, it is comprised of two major antiparallel beta-sheets, designated ABED and CFG. For the C2-domain, there are two additional strands on the CFG sheet. Furthermore, sheets ABED and CFG are interconnected by several cross-connecting loops and one alpha-helix (DH1). The side chains of D982 and N996 in the C2-domain are involved in hydrogen bonding with the side chains of R1264 and N1295 in the C3 domain. Main chain hydrogen bonding can also be observed between S992 in C2 and N1189/G1191 in C3, furthermore stabilizing the interaction between the domains. The C2 domain contains one bound metal ion, modeled as Ca2+, and both the C2- and C3-domains are stabilized by conserved isopeptide bonds, which connect the beta-sheets of the central DEv-IgG motifs [1].Other members of this family include Major cell-surface adhesin PAc from Streptococcus mutans and SspB from Streptococcus gordonii.
Literature references
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Hall M, Nylander S, Jenkinson HF, Persson K;, FEBS Open Bio. 2014;4:283-289.: Structure of the C-terminal domain of AspA (antigen I/II-family) protein from Streptococcus pyogenes. PUBMED:24918040 EPMC:24918040
Internal database links
SCOOP: | Antigen_C |
Similarity to PfamA using HHSearch: | Antigen_C |
This tab holds annotation information from the InterPro database.
InterPro entry IPR026345
This entry represents a domain with a conserved Lys and Asn that form an intramolecular isopeptide bond [ PUBMED:20138058 ]. The domain is found in a variety of proteins, including cell-surface adhesins and members of the Antigen I/II family.
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 Adhesin (CL0204), which has the following description:
This superfamily includes a variety of bacterial adhesins that have a jelly-roll beta-barrel fold [1]. These domains are involved in sugar recognition.
The clan contains the following 17 members:
Adhesin_Dr AfaD AgI_II_C2 Antig_Caf1 Antigen_C Collagen_bind DUF1120 Fim-adh_lectin FimA Fimbrial FimH_man-bind GramPos_pilinBB PapG_N Saf-Nte_pilin SCPU SdrG_C_C Sgo0707_N2Alignments
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 (41) |
Full (173) |
Representative proteomes | UniProt (3550) |
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RP15 (5) |
RP35 (40) |
RP55 (172) |
RP75 (448) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (41) |
Full (173) |
Representative proteomes | UniProt (3550) |
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RP15 (5) |
RP35 (40) |
RP55 (172) |
RP75 (448) |
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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: | ECOD:EUF00480 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
El-Gebali S |
Number in seed: | 41 |
Number in full: | 173 |
Average length of the domain: | 159.3 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 22.23 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 167 | ||||||||||||
Family (HMM) version: | 4 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 AgI_II_C2 domain has been found. There are 21 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 |
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A8AUS0 | View 3D Structure | Click here |
A8AUS1 | View 3D Structure | Click here |
P17953 | View 3D Structure | Click here |
P23504 | View 3D Structure | Click here |