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.
14  structures 440  species 1  interaction 466  sequences 29  architectures

Family: Rap1_C (PF11626)

Summary: TRF2-interacting telomeric protein/Rap1 - C terminal domain

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.

TRF2-interacting telomeric protein/Rap1 - C terminal domain Provide feedback

This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres [1]. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain [1]. Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms [2,3,4,5]. Model doesn't capture Sch. pombe as it cuts this sequence into two.

Literature references

  1. Feeser EA, Wolberger C; , J Mol Biol. 2008;380:520-531.: Structural and functional studies of the Rap1 C-terminus reveal novel separation-of-function mutants. PUBMED:18538788 EPMC:18538788

  2. Ye JZ, Donigian JR, van Overbeek M, Loayza D, Luo Y, Krutchinsky AN, Chait BT, de Lange T; , J Biol Chem 2004;279:47264-47271.: TIN2 binds TRF1 and TRF2 simultaneously and stabilizes the TRF2 complex on telomeres. PUBMED:15316005 EPMC:15316005

  3. de Lange T;, Genes Dev. 2005;19:2100-2110.: Shelterin: the protein complex that shapes and safeguards human telomeres. PUBMED:16166375 EPMC:16166375

  4. Sfeir A, Kabir S, van Overbeek M, Celli GB, de Lange T;, Science. 2010;327:1657-1661.: Loss of Rap1 induces telomere recombination in the absence of NHEJ or a DNA damage signal. PUBMED:20339076 EPMC:20339076

  5. Martinez P, Thanasoula M, Carlos AR, Gomez-Lopez G, Tejera AM, Schoeftner S, Dominguez O, Pisano DG, Tarsounas M, Blasco MA;, Nat Cell Biol. 2010;12:768-780.: Mammalian Rap1 controls telomere function and gene expression through binding to telomeric and extratelomeric sites. PUBMED:20622869 EPMC:20622869

  6. Chen Y, Rai R, Zhou ZR, Kanoh J, Ribeyre C, Yang Y, Zheng H, Damay P, Wang F, Tsujii H, Hiraoka Y, Shore D, Hu HY, Chang S, Lei M;, Nat Struct Mol Biol. 2011;18:213-221.: A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms. PUBMED:21217703 EPMC:21217703

  7. Fujita I, Tanaka M, Kanoh J;, PLoS One. 2012;7:e49151.: Identification of the functional domains of the telomere protein Rap1 in Schizosaccharomyces pombe. PUBMED:23133674 EPMC:23133674


This tab holds annotation information from the InterPro database.

InterPro entry IPR021661

This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres [PUBMED:18538788]. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain [PUBMED:18538788]. Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms [PUBMED:15316005, PUBMED:16166375, PUBMED:20339076, PUBMED:20622869].

Domain organisation

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

Loading domain graphics...

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
(78)
Full
(466)
Representative proteomes UniProt
(642)
NCBI
(824)
Meta
(1)
RP15
(74)
RP35
(203)
RP55
(337)
RP75
(465)
Jalview View  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
(78)
Full
(466)
Representative proteomes UniProt
(642)
NCBI
(824)
Meta
(1)
RP15
(74)
RP35
(203)
RP55
(337)
RP75
(465)
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
(78)
Full
(466)
Representative proteomes UniProt
(642)
NCBI
(824)
Meta
(1)
RP15
(74)
RP35
(203)
RP55
(337)
RP75
(465)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: pdb_3cz6
Previous IDs: Rap1_C; TRF2IP; Yippee-Rap1;
Type: Family
Sequence Ontology: SO:0100021
Author: Pollington J
Number in seed: 78
Number in full: 466
Average length of the domain: 86.80 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 13.49 %

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 23.8 23.8
Trusted cut-off 23.8 23.9
Noise cut-off 23.7 23.7
Model length: 84
Family (HMM) version: 8
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.

Interactions

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

Rap1_C

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 Rap1_C domain has been found. There are 14 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.

Loading structure mapping...