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15  structures 133  species 1  interaction 389  sequences 10  architectures

Family: Intimin_C (PF07979)

Summary: Intimin C-type lectin domain

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Intimin Edit Wikipedia article

Intimin C-type lectin domain
PDB 1e5u EBI.jpg
nmr representative structure of intimin-190 (int190) from enteropathogenic e. coli
Identifiers
Symbol Intimin_C
Pfam PF07979
Pfam clan CL0056
InterPro IPR013117

Intimin is a virulence factor (adhesin) of EPEC (e.g. E. coli O127:H6) and EHEC (e.g. E. coli O157:H7) E. coli strains. It is an attaching and effacing (A/E) protein which with other virulence factors is responsible for enteropathogenic and enterohaemorrhagic diarrhoea.[1]

Intimin is expressed on the bacterial cell surface where it can bind to its receptor Tir (Translocated intimin receptor). Tir, along with over 25 other bacterial proteins, is secreted from attaching and effacing E. coli directly into the cytoplasm of intestinal epithelial cells by a Type three secretion system. Once within the cytoplasm of the host cell, Tir is inserted into the plasma membrane, allowing surface exposure and intimin binding.[1]

The structure of the C-terminal domain has been solved and shown to have a C-lectin type of structure.[2]

References[edit]

  1. ^ a b Stevens, J. et al. (2006). "Actin-dependent movement of bacterial pathogens". Nature Reviews Microbiology 4: 91–101. doi:10.1038/nrmicro1320. PMID 16415925. 
  2. ^ Batchelor M, Prasannan S, Daniell S, Reece S, Connerton I, Bloomberg G, Dougan G, Frankel G, Matthews S (June 2000). "Structural basis for recognition of the translocated intimin receptor (Tir) by intimin from enteropathogenic Escherichia coli". EMBO J. 19 (11): 2452–64. doi:10.1093/emboj/19.11.2452. PMC 212744. PMID 10835344. 

This article incorporates text from the public domain Pfam and InterPro IPR013117


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.

Intimin C-type lectin domain Provide feedback

This domain is found at the C-terminus of intimin. Its structure has been solved and shown to have a C-lectin type of structure [1]. Intimin is a bacterial adhesion molecule involved in intimate attachment of enteropathogenic and enterohemorrhagic Escherichia coli to mammalian host cells. Intimin targets the translocated intimin receptor (Tir), which is exported by the bacteria and integrated into the host cell plasma membrane.

Literature references

  1. Batchelor M, Prasannan S, Daniell S, Reece S, Connerton I, Bloomberg G, Dougan G, Frankel G, Matthews S; , EMBO J 2000;19:2452-2464.: Structural basis for recognition of the translocated intimin receptor (Tir) by intimin from enteropathogenic Escherichia coli. PUBMED:10835344 EPMC:10835344


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013117

This domain is found at the C terminus of intimin. Its structure has been solved and shown to have a C-lectin type of structure [PUBMED:10835344]. Intimin is a bacterial adhesion molecule involved in intimate attachment of enteropathogenic and enterohemorrhagic Escherichia coli to mammalian host cells. Intimin targets the translocated intimin receptor (Tir), which is exported by the bacteria and integrated into the host cell plasma membrane.

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 C_Lectin (CL0056), which has the following description:

This clan contains domains that have a C-type lectin fold. Many of these are known or expected to mediate interactions with sugars.

The clan contains the following 7 members:

APT C4 Chordopox_A33R Herpes_UL45 Intimin_C Lectin_C Xlink

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.

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(14)
Full
(389)
Representative proteomes NCBI
(312)
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(0)
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(0)
RP35
(0)
RP55
(1)
RP75
(2)
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Format an alignment

  Seed
(14)
Full
(389)
Representative proteomes NCBI
(312)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(2)
Alignment:
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  Seed
(14)
Full
(389)
Representative proteomes NCBI
(312)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(2)
Raw Stockholm Download   Download       Download   Download   Download    
Gzipped 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.

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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_1879 (Release 16.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 14
Number in full: 389
Average length of the domain: 94.00 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 12.60 %

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 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 101
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Big_2

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 Intimin_C domain has been found. There are 15 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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