Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 21  species 0  interactions 131  sequences 4  architectures

Family: Claudin_3 (PF06653)

Summary: Tight junction protein, Claudin-like

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Claudin". More...

Claudin Edit Wikipedia article

For the Arthurian character, see Prince Claudin. For the French composer, see Claudin de Sermisy.
Cellular tight junction-en.svg
PMP22_Claudin
Identifiers
Symbol PMP22_Claudin
Pfam PF00822
Pfam clan CL0375
InterPro IPR004031
PROSITE PDOC01045
TCDB 1.H.1
OPM superfamily 492
OPM protein 4p79

Claudins are a family of proteins that are the most important components of the tight junctions, where they establish the paracellular barrier that controls the flow of molecules in the intercellular space between the cells of an epithelium. They have four transmembrane domains, with the N-terminus and the C-terminus in the cytoplasm.

Structure

Claudins are small (20–27 kilodalton (kDa)) transmembrane proteins which are found in many organisms, ranging from nematodes to human beings, and are very similar in their structure, although this conservation is not observed on the genetic level. Claudins span the cellular membrane 4 times, with the N-terminal end and the C-terminal end both located in the cytoplasm, and two extracellular loops which show the highest degree of conservation. The first extracellular loop consists on average of 53 amino acids and the second one, being slightly smaller, of 24 amino acids. The N-terminal end is usually very short (4–10 amino acids), the C-terminal end varies in length from 21 to 63 and is necessary for the localisation of these proteins in the tight junctions.[1] It is suspected that the cysteines of individual or separate claudins form disulfide bonds. All human claudins (with the exception of Claudin 12) have domains that let them bind to PDZ domains of scaffold proteins.

History

Claudins were first named in 1998 by Japanese researchers Mikio Furuse and Shoichiro Tsukita at Kyoto University.[2] The name claudin comes from Latin word claudere ("to close"), suggesting the barrier role of these proteins.

A recent review discusses evidence regarding the structure and function of claudin family proteins using a systems approach to understand evidence generated by proteomics techniques.[3]

Genes

In humans, 24 members of the family have been described.

See also

Additional images

References

  1. ^ Rüffer C, Gerke V (May 2004). "The C-terminal cytoplasmic tail of claudins 1 and 5 but not its PDZ-binding motif is required for apical localization at epithelial and endothelial tight junctions". Eur. J. Cell Biol. 83 (4): 135–44. doi:10.1078/0171-9335-00366. PMID 15260435. 
  2. ^ Furuse M, Fujita K, Hiiragi T, Fujimoto K, Tsukita S (June 1998). "Claudin-1 and -2: novel integral membrane proteins localizing at tight junctions with no sequence similarity to occludin". J. Cell Biol. 141 (7): 1539–50. doi:10.1083/jcb.141.7.1539. PMC 2132999. PMID 9647647. 
  3. ^ Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS (Dec 2015). "A systems proteomics view of the endogenous human claudin protein family". J Proteome Res. doi:10.1021/acs.jproteome.5b00769. PMID 26680015. 

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.

Tight junction protein, Claudin-like Provide feedback

This is a family of probable membrane tight junction, Claudin-like, proteins.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009545

This is a family of probable membrane tight junction, claudin-like, proteins.

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan Transporter (CL0375), which has the following description:

The members of this superfamily are probably all transporter protein domains. All families normally carry four tansmembrane regions, which in many instances associate into hexameric structures. They are frequently involved in gap-junction formation between cells or in forming pores linking the cytosol with the extracellulare space 1,2]. The clan includes members of the TCDB superfamilies 1.A.24 and 1.A.25.

The clan contains the following 12 members:

Amastin Claudin_2 Claudin_3 Clc-like Connexin Fig1 GSG-1 Innexin L_HMGIC_fpl Pannexin_like PMP22_Claudin SUR7

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(24)
Full
(131)
Representative proteomes UniProt
(162)
NCBI
(198)
Meta
(0)
RP15
(50)
RP35
(66)
RP55
(128)
RP75
(128)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(24)
Full
(131)
Representative proteomes UniProt
(162)
NCBI
(198)
Meta
(0)
RP15
(50)
RP35
(66)
RP55
(128)
RP75
(128)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(24)
Full
(131)
Representative proteomes UniProt
(162)
NCBI
(198)
Meta
(0)
RP15
(50)
RP35
(66)
RP55
(128)
RP75
(128)
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.

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_21553 (release 10.0)
Previous IDs: DUF1164;
Type: Family
Author: Moxon SJ, Coggill P
Number in seed: 24
Number in full: 131
Average length of the domain: 160.50 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 90.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.1 26.1
Trusted cut-off 26.1 26.1
Noise cut-off 26.0 25.9
Model length: 164
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.