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49  structures 4043  species 6  interactions 40364  sequences 3  architectures

Family: SSL_OB (PF09199)

Summary: Staphylococcal superantigen-like OB-fold domain

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Staphylococcal superantigen-like OB-fold domain Provide feedback

This OB-fold domain folds into a five-stranded beta-barrel [1]. Members of this family are found in various staphylococcal toxins described as staphylococcal superantigen-like (SSL) proteins that are related to the staphylococcal enterotoxins (SEs) or superantigens. These SSL proteins of which 11 have so far been characterised have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold), this domain, linked to a beta-grasp domain, family Stap_Strp_tox_C, PF02876. SSLs do not bind to T-cell receptors or major histocompatibility complex class II molecules and do not stimulate T cells. SSLs target components of innate immunity, such as complement, Fc receptors, and myeloid cells 2,3,4,5,6,7,8]. SSL protein 7 (SSL7) is the best characterised of the SSLs and binds complement factor C5 and IgA with high affinity and inhibits the end stage of complement activation and IgA binding to FcαR [8].

Literature references

  1. Arcus VL, Langley R, Proft T, Fraser JD, Baker EN; , J Biol Chem. 2002;277:32274-32281.: The Three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome. PUBMED:12082105 EPMC:12082105

  2. Al-Shangiti AM, Naylor CE, Nair SP, Briggs DC, Henderson B, Chain BM;, Infect Immun. 2004;72:4261-4270.: Structural relationships and cellular tropism of staphylococcal superantigen-like proteins. PUBMED:15213171 EPMC:15213171

  3. Ramsland PA, Willoughby N, Trist HM, Farrugia W, Hogarth PM, Fraser JD, Wines BD;, Proc Natl Acad Sci U S A. 2007;104:15051-15056.: Structural basis for evasion of IgA immunity by Staphylococcus aureus revealed in the complex of SSL7 with Fc of human IgA1. PUBMED:17848512 EPMC:17848512

  4. Baker HM, Basu I, Chung MC, Caradoc-Davies T, Fraser JD, Baker EN;, J Mol Biol. 2007;374:1298-1308.: Crystal structures of the staphylococcal toxin SSL5 in complex with sialyl Lewis X reveal a conserved binding site that shares common features with viral and bacterial sialic acid binding proteins. PUBMED:17996251 EPMC:17996251

  5. Chung MC, Wines BD, Baker H, Langley RJ, Baker EN, Fraser JD;, Mol Microbiol. 2007;66:1342-1355.: The crystal structure of staphylococcal superantigen-like protein 11 in complex with sialyl Lewis X reveals the mechanism for cell binding and immune inhibition. PUBMED:18045383 EPMC:18045383

  6. Laursen NS, Gordon N, Hermans S, Lorenz N, Jackson N, Wines B, Spillner E, Christensen JB, Jensen M, Fredslund F, Bjerre M, Sottrup-Jensen L, Fraser JD, Andersen GR;, Proc Natl Acad Sci U S A. 2010;107:3681-3686.: Structural basis for inhibition of complement C5 by the SSL7 protein from Staphylococcus aureus. PUBMED:20133685 EPMC:20133685

  7. Laursen NS, Andersen KR, Braren I, Spillner E, Sottrup-Jensen L, Andersen GR;, EMBO J. 2011;30:606-616.: Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex. PUBMED:21217642 EPMC:21217642

  8. Hermans SJ, Baker HM, Sequeira RP, Langley RJ, Baker EN, Fraser JD;, Infect Immun. 2012;80:4004-4013.: Structural and functional properties of staphylococcal superantigen-like protein 4. PUBMED:22949551 EPMC:22949551

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015282

This domain is found in various staphylococcal toxins, and adopts an OB fold, wherein the domain folds into a five-stranded beta-barrel. The exact manner in which they confer pathogenic properties to the protein has not, as yet, been determined [PUBMED:12082105].

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 OB (CL0021), which has the following description:

The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].

The clan contains the following 49 members:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_aCoA_assoc OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RsgA_N RuvA_N S1 S1-like S1_2 SSB SSL_OB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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: pdb_1m4v
Previous IDs: DUF1954;
Type: Domain
Author: Sammut SJ
Number in seed: 11
Number in full: 40364
Average length of the domain: 83.20 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 33.73 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 21.5 21.3
Noise cut-off 20.7 19.7
Model length: 84
Family (HMM) version: 6
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


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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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There are 6 interactions for this family. More...

A2M SSL_OB Stap_Strp_tox_C Stap_Strp_tox_C C1-set Ig_2


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 SSL_OB domain has been found. There are 49 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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