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6  structures 29  species 0  interactions 29  sequences 2  architectures

Family: T3SSipB (PF16535)

Summary: Type III cell invasion protein SipB

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Type III cell invasion protein SipB Provide feedback

T3SSipB is a family of pathogenic Gram-negative bacterial proteins that invade human intestinal cells via the type III secretion system translocators. T3SSipB represents the coiled -coil region of the proteins and is shown to be homologous in activity to the pore-forming toxins of other Gram-negative pathogens, such as colicin Ia [1-8].

Literature references

  1. Hermant D, Menard R, Arricau N, Parsot C, Popoff MY;, Mol Microbiol. 1995;17:781-789.: Functional conservation of the Salmonella and Shigella effectors of entry into epithelial cells. PUBMED:8801431 EPMC:8801431

  2. Kaniga K, Tucker S, Trollinger D, Galan JE;, J Bacteriol. 1995;177:3965-3971.: Homologs of the Shigella IpaB and IpaC invasins are required for Salmonella typhimurium entry into cultured epithelial cells. PUBMED:7608068 EPMC:7608068

  3. Hersh D, Monack DM, Smith MR, Ghori N, Falkow S, Zychlinsky A;, Proc Natl Acad Sci U S A. 1999;96:2396-2401.: The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. PUBMED:10051653 EPMC:10051653

  4. Hayward RD, McGhie EJ, Koronakis V;, Mol Microbiol. 2000;37:727-739.: Membrane fusion activity of purified SipB, a Salmonella surface protein essential for mammalian cell invasion. PUBMED:10972796 EPMC:10972796

  5. Hernandez LD, Pypaert M, Flavell RA, Galan JE;, J Cell Biol. 2003;163:1123-1131.: A Salmonella protein causes macrophage cell death by inducing autophagy. PUBMED:14662750 EPMC:14662750

  6. Suparak S, Kespichayawattana W, Haque A, Easton A, Damnin S, Lertmemongkolchai G, Bancroft GJ, Korbsrisate S;, J Bacteriol. 2005;187:6556-6560.: Multinucleated giant cell formation and apoptosis in infected host cells is mediated by Burkholderia pseudomallei type III secretion protein BipB. PUBMED:16159789 EPMC:16159789

  7. Asakura H, Ekawa T, Sugimoto N, Momose Y, Kawamoto K, Makino S, Igimi S, Yamamoto S;, Biochem Biophys Res Commun. 2012;426:654-658.: Membrane topology of Salmonella invasion protein SipB confers osmotolerance. PUBMED:22975346 EPMC:22975346

  8. Barta ML, Dickenson NE, Patil M, Keightley A, Wyckoff GJ, Picking WD, Picking WL, Geisbrecht BV;, J Mol Biol. 2012;417:395-405.: The structures of coiled-coil domains from type III secretion system translocators reveal homology to pore-forming toxins. PUBMED:22321794 EPMC:22321794


This tab holds annotation information from the InterPro database.

InterPro entry IPR032391

This entry represents the N-terminal coiled-coil region of the invasin IpaB, which is a pathogenic Gram-negative bacterial protein that invades human intestinal cells via the type III secretion system translocators. This domain is homologous in activity to the pore-forming toxins of other Gram-negative pathogens, such as colicin Ia [PUBMED:8801431, PUBMED:22321794].

Domain organisation

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Alignments

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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
(5)
Full
(29)
Representative proteomes UniProt
(383)
NCBI
(686)
Meta
(0)
RP15
(1)
RP35
(7)
RP55
(25)
RP75
(86)
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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
(5)
Full
(29)
Representative proteomes UniProt
(383)
NCBI
(686)
Meta
(0)
RP15
(1)
RP35
(7)
RP55
(25)
RP75
(86)
Alignment:
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Sequence:
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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
(5)
Full
(29)
Representative proteomes UniProt
(383)
NCBI
(686)
Meta
(0)
RP15
(1)
RP35
(7)
RP55
(25)
RP75
(86)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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.

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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_3tul
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 5
Number in full: 29
Average length of the domain: 153.30 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 25.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 31.0 31.0
Trusted cut-off 31.2 31.2
Noise cut-off 30.9 30.6
Model length: 155
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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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 T3SSipB domain has been found. There are 6 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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