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21  structures 165  species 1  interaction 1484  sequences 69  architectures

Family: B (PF02216)

Summary: B domain

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This is the Wikipedia entry entitled "SpAB protein domain". More...

SpAB protein domain Edit Wikipedia article

SpAB protein domain
PDB 1ss1 EBI.jpg
Staphylococcal protein a, b-domain
Identifiers
Symbol B
Pfam PF02216
InterPro IPR003132
SMART TBC
PROSITE PDOC00957
MEROPS S12
SCOP 1ehx
SUPERFAMILY 1ehx
TCDB 9.B.4
CAZy GH58

In molecular biology, the domain B, refers to the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Hence, it is abbreviated to SpAB.

Function[edit]

SpAB enables theStaphylococcus aureus bacteria to evade the host's immune system through the disruption of opsonization and phagocytosis. It does this though SpAB binding to the Fc fragment of IgG.

Structure[edit]

The B domain of SpA (SpAB) consists of three a-helices which are retained upon interaction with the Fc fragment of IgG. Protein A contains five highly homologous immunoglobulin (Ig)-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition).[1]

The native state of the B domain, deviates a lot since its inter-helical angles fluctuate. It appears to be relatively thermodynamically more stable than the E domain. The increased stability of the B domain may be due to heightened mobility, and therefore entropy, in the native state and decreased mobility entropy in the more compact denatured state. [2]

References[edit]

  1. ^ Graille M, Stura EA, Corper AL, Sutton BJ, Taussig MJ, Charbonnier JB, Silverman GJ (May 2000). "Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity". Proc. Natl. Acad. Sci. U.S.A. 97 (10): 5399–404. doi:10.1073/pnas.97.10.5399. PMC 25840. PMID 10805799. 
  2. ^ Alonso DO, Daggett V (2000). "Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains.". Proc Natl Acad Sci U S A 97 (1): 133–8. PMC 26628. PMID 10618383. 

This article incorporates text from the public domain Pfam and InterPro IPR003132

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.

B domain Provide feedback

This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.

Literature references

  1. Gouda H, Torigoe H, Saito A, Sato M, Arata Y, Shimada I; , Biochemistry 1992;31:9665-9672.: Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. PUBMED:1390743 EPMC:1390743


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003132

This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [PUBMED:10805799].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(6)
Full
(1484)
Representative proteomes NCBI
(1155)
Meta
(0)
RP15
(8)
RP35
(8)
RP55
(12)
RP75
(12)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(6)
Full
(1484)
Representative proteomes NCBI
(1155)
Meta
(0)
RP15
(8)
RP35
(8)
RP55
(12)
RP75
(12)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(6)
Full
(1484)
Representative proteomes NCBI
(1155)
Meta
(0)
RP15
(8)
RP35
(8)
RP55
(12)
RP75
(12)
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.

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.

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: Pfam-B_1782 (release 5.2)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 6
Number in full: 1484
Average length of the domain: 53.40 aa
Average identity of full alignment: 62 %
Average coverage of the sequence by the domain: 43.70 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.9 22.4
Noise cut-off 21.5 22.3
Model length: 54
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

C1-set

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 B 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 seqence.

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