Summary: Double-stranded RNA binding motif
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Double-stranded RNA binding motif Provide feedback
Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.
Literature references
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Burd CG, Dreyfuss G; , Science 1994;265:615-621.: Conserved structures and diversity of functions of RNA-binding proteins. PUBMED:8036511 EPMC:8036511
Internal database links
SCOOP: | APO_RNA-bind Dicer_dimer DND1_DSRM |
Similarity to PfamA using HHSearch: | Dicer_dimer DND1_DSRM |
External database links
HOMSTRAD: | dsrm |
SCOP: | 1stu |
This tab holds annotation information from the InterPro database.
InterPro entry IPR014720
In contrast to other RNA-binding domains, the about 65 amino acids long dsRBD domain [PUBMED:1438302, PUBMED:8036511, PUBMED:7972084] has been found in a number of proteins that specifically recognise double-stranded RNAs. The dsRBD domain is also known as DSRM (Double-Stranded RNA-binding Motif). dsRBD proteins are mainly involved in posttranscriptional gene regulation, for example by preventing the expression of proteins or by mediating RNAs localization. This domain is also found in RNA editing proteins. Interaction of the dsRBD with RNA is unlikely to involve the recognition of specific sequences [PUBMED:1357546, PUBMED:7527340, PUBMED:8127710]. Nevertheless, multiple dsRBDs may be able to act in combination to recognise the secondary structure of specific RNAs (i.e. Staufen) [PUBMED:1438302]. NMR analysis of the third dsRBD of Drosophila Staufen have revealed an alpha-beta-beta-beta-alpha structure [PUBMED:7628456].
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 DSRM (CL0196), which has the following description:
This clan contains RNA-binding domains.
The clan contains the following 9 members:
Dicer_dimer Dicer_N DND1_DSRM dsRBD2 dsrm LIX1 Rad52_Rad22 Ribosomal_S5 Staufen_CAlignments
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...
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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 (77) |
Full (23846) |
Representative proteomes | UniProt (59760) |
NCBI (83634) |
Meta (1682) |
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RP15 (2864) |
RP35 (9249) |
RP55 (18234) |
RP75 (28628) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (77) |
Full (23846) |
Representative proteomes | UniProt (59760) |
NCBI (83634) |
Meta (1682) |
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RP15 (2864) |
RP35 (9249) |
RP55 (18234) |
RP75 (28628) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Published_alignment |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Eddy SR |
Number in seed: | 77 |
Number in full: | 23846 |
Average length of the domain: | 65.10 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 18.56 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 67 | ||||||||||||
Family (HMM) version: | 27 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 dsrm domain has been found. There are 118 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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