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29  structures 1249  species 0  interactions 3998  sequences 58  architectures

Family: Tctex-1 (PF03645)

Summary: Tctex-1 family

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Tctex-1 family Provide feedback

Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.

Literature references

  1. Lader E, Ha HS, O'Neill M, Artzt K, Bennett D; , Cell 1989;58:969-979.: tctex-1: a candidate gene family for a mouse t complex sterility locus. PUBMED:2570638 EPMC:2570638

  2. Tai AW, Chuang JZ, Bode C, Wolfrum U, Sung CH; , Cell 1999;97:877-887.: Rhodopsin's carboxy-terminal cytoplasmic tail acts as a membrane receptor for cytoplasmic dynein by binding to the dynein light chain Tctex-1. PUBMED:10399916 EPMC:10399916


This tab holds annotation information from the InterPro database.

InterPro entry IPR005334

Tctex-1 is a dynein light chain. Dynein translocates rhodopsin-bearing vesicles along microtubules and it has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin for retrograde or apical transport [ PUBMED:15701632 ]. An efficient vectorial transport system must be required to deliver large numbers of newly synthesised rhodopsin molecules (~10 7 molecules per day per photoreceptor) to the base of the outer segment of the photoreceptor, Tctex-1 may well play a role in this process. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit the interaction between Tctex-1 and rhodopsin, which may be the molecular basis of retinitis pigmentosa [ PUBMED:10399916 ].

In the mouse, the chromosomal location and pattern of expression of Tctex-1 make it a candidate for involvement in male sterility [ PUBMED:2570638 ].

This entry also includes Topoisomerase I damage affected protein 2 (TDA2) whose crystal structure revealed that it belongs to the dynein light chain family. It is part of the endocytic machinery and required for normal internalisation of native cargo in yeast [ PUBMED:28706108 ].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(286)
Full
(3998)
Representative proteomes UniProt
(7194)
RP15
(1037)
RP35
(1865)
RP55
(3147)
RP75
(4075)
Jalview 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
(286)
Full
(3998)
Representative proteomes UniProt
(7194)
RP15
(1037)
RP35
(1865)
RP55
(3147)
RP75
(4075)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(286)
Full
(3998)
Representative proteomes UniProt
(7194)
RP15
(1037)
RP35
(1865)
RP55
(3147)
RP75
(4075)
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.

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_2986 (release 7.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 286
Number in full: 3998
Average length of the domain: 97.1 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 60.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.9 22.8
Noise cut-off 22.6 22.7
Model length: 94
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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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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 Tctex-1 domain has been found. There are 29 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044STI9 View 3D Structure Click here
A0A044V8X8 View 3D Structure Click here
A0A077YX91 View 3D Structure Click here
A0A077YYF8 View 3D Structure Click here
A0A0B4LEE2 View 3D Structure Click here
A0A0D2DXQ5 View 3D Structure Click here
A0A0G2K5Q6 View 3D Structure Click here
A0A0K0E4R4 View 3D Structure Click here
A0A0K0EEI4 View 3D Structure Click here
A0A0N4UEH6 View 3D Structure Click here
A0A175WEC7 View 3D Structure Click here
A0A1C1CUL1 View 3D Structure Click here
A0A1D8PGQ1 View 3D Structure Click here
A0A1U7F4D5 View 3D Structure Click here
A0A2R8QA44 View 3D Structure Click here
A0A3P7DL45 View 3D Structure Click here
A0A3P7E8L8 View 3D Structure Click here
A0A5K4EQ73 View 3D Structure Click here
A0A5K4F1M9 View 3D Structure Click here
A0A5K4F5G5 View 3D Structure Click here
A0A5K4FBU2 View 3D Structure Click here
A4HSG4 View 3D Structure Click here
A4HVP6 View 3D Structure Click here
A4HXU8 View 3D Structure Click here
A4I3H2 View 3D Structure Click here
A4IBH9 View 3D Structure Click here
A7TTT7 View 3D Structure Click here
C0H4G0 View 3D Structure Click here
C0H568 View 3D Structure Click here
C0NMQ8 View 3D Structure Click here
C1GYH5 View 3D Structure Click here
C4Y8K5 View 3D Structure Click here
C5DTH5 View 3D Structure Click here
C6S3G7 View 3D Structure Click here
D3Z8A1 View 3D Structure Click here
D3ZD38 View 3D Structure Click here
F1Q5L5 View 3D Structure Click here
F1QMY1 View 3D Structure Click here
G3V8D8 View 3D Structure Click here
G4LZ86 View 3D Structure Click here