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1  structure 217  species 0  interactions 491  sequences 58  architectures

Family: Dicer_dimer (PF03368)

Summary: Dicer dimerisation 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.

Dicer dimerisation domain Provide feedback

This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer [1,2]. It is a divergent double stranded RNA-binding domain [3]. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity [4]. This domain has weak dsRNA-binding activity. It mediates heterodimerisation of Dicer proteins with their respective protein partners [4].

Literature references

  1. Lee Y, Hur I, Park SY, Kim YK, Suh MR, Kim VN;, EMBO J. 2006;25:522-532.: The role of PACT in the RNA silencing pathway. PUBMED:16424907 EPMC:16424907

  2. Ye X, Paroo Z, Liu Q;, J Biol Chem. 2007;282:28373-28378.: Functional anatomy of the Drosophila microRNA-generating enzyme. PUBMED:17666393 EPMC:17666393

  3. Dlakic M; , Bioinformatics. 2006;22:2711-2714.: DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold. PUBMED:16954143 EPMC:16954143

  4. Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA;, RNA. 2010;16:474-481.: Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. PUBMED:20106953 EPMC:20106953


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005034

This domain is found in members of the Dicer protein family of dsRNA nucleases. This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PROSITEDOC), a domain of unknown function, and a PAZ domain (PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [PUBMED:16410517, PUBMED:16954143, PUBMED:17277330, PUBMED:17666393].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(29)
Full
(491)
Representative proteomes NCBI
(546)
Meta
(1)
RP15
(93)
RP35
(165)
RP55
(251)
RP75
(308)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(29)
Full
(491)
Representative proteomes NCBI
(546)
Meta
(1)
RP15
(93)
RP35
(165)
RP55
(251)
RP75
(308)
Alignment:
Format:
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Sequence:
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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
(29)
Full
(491)
Representative proteomes NCBI
(546)
Meta
(1)
RP15
(93)
RP35
(165)
RP55
(251)
RP75
(308)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Bateman A
Previous IDs: DUF283; dsRNA_bind;
Type: Domain
Author: Bateman A, Mistry J, Eberhardt R
Number in seed: 29
Number in full: 491
Average length of the domain: 94.40 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 5.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 23.1 22.7
Noise cut-off 22.5 22.5
Model length: 91
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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 Dicer_dimer domain has been found. There are 1 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 seqence.

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