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2  structures 101  species 0  interactions 1167  sequences 23  architectures

Family: RST (PF12174)

Summary: RCD1-SRO-TAF4 (RST) plant domain

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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.

RCD1-SRO-TAF4 (RST) plant domain Provide feedback

This domain is found in plant RCD1, SRO and TAF4 proteins, hence its name of RST. It is required for interaction with multiple plant transcription factors. Radical-Induced Cell Death1 (RCD1) is an important regulator of stress and hormonal and developmental responses in Arabidopsis thaliana, as is its closest homologue, SRO1 - Similar To RCD-One1. TBP-Associated Factor 4 (TAF4) and TAF4-b are components of the transcription initiation factor complex TFIID.

Literature references

  1. Belles-Boix E, Babiychuk E, Van Montagu M, Inze D, Kushnir S;, FEBS Lett. 2000;482:19-24.: CEO1, a new protein from Arabidopsis thaliana, protects yeast against oxidative damage. PUBMED:11018516 EPMC:11018516

  2. Ahlfors R, Lang S, Overmyer K, Jaspers P, Brosche M, Tauriainen A, Kollist H, Tuominen H, Belles-Boix E, Piippo M, Inze D, Palva ET, Kangasjarvi J;, Plant Cell. 2004;16:1925-1937.: Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses. PUBMED:15208394 EPMC:15208394

  3. Marr MT 2nd;, Proc Natl Acad Sci U S A. 2009;106:1295-1296: TAF4 takes flight. PUBMED:19174510 EPMC:19174510

  4. Jaspers P, Blomster T, Brosche M, Salojarvi J, Ahlfors R, Vainonen JP, Reddy RA, Immink R, Angenent G, Turck F, Overmyer K, Kangasjarvi J;, Plant J. 2009;60:268-279.: Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. PUBMED:19548978 EPMC:19548978

  5. Jaspers P, Overmyer K, Wrzaczek M, Vainonen JP, Blomster T, Salojarvi J, Reddy RA, Kangasjarvi J;, BMC Genomics. 2010;11:170.: The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. PUBMED:20226034 EPMC:20226034


This tab holds annotation information from the InterPro database.

InterPro entry IPR022003

This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.

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, 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
(49)
Full
(1167)
Representative proteomes UniProt
(1632)
NCBI
(2460)
Meta
(0)
RP15
(48)
RP35
(601)
RP55
(941)
RP75
(1181)
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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
(49)
Full
(1167)
Representative proteomes UniProt
(1632)
NCBI
(2460)
Meta
(0)
RP15
(48)
RP35
(601)
RP55
(941)
RP75
(1181)
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
(49)
Full
(1167)
Representative proteomes UniProt
(1632)
NCBI
(2460)
Meta
(0)
RP15
(48)
RP35
(601)
RP55
(941)
RP75
(1181)
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_8550 (release 23.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Overmyer K , Coggill P
Number in seed: 49
Number in full: 1167
Average length of the domain: 64.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 10.89 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.7 22.7
Trusted cut-off 22.9 23.0
Noise cut-off 22.6 22.5
Model length: 67
Family (HMM) version: 9
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 RST domain has been found. There are 2 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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