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5  structures 18928  species 2  interactions 19474  sequences 32  architectures

Family: Ribonucleas_3_3 (PF14622)

Summary: Ribonuclease-III-like

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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.

Ribonuclease-III-like Provide feedback

Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000999

Prokaryotic ribonuclease III (EC) (gene rnc) [PUBMED:3903434] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related to a number of proteins including [PUBMED:9241229]:

  • Saccharomyces cerevisiae (Baker's yeast) protein pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development
  • yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites
  • Caenorhabditis elegans hypothetical protein F26E4.13
  • Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R
  • Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346
  • yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain
  • C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c

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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Pfam Clan

This family is a member of clan RNase_III (CL0539), which has the following description:

This superfamily is characterised structurally by having a core of 5 helices where one of the helices is surrounded by the others. Many members have the endonuclease catalytic domain.

The clan contains the following 3 members:

Ribonucleas_3_2 Ribonucleas_3_3 Ribonuclease_3


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.

Representative proteomes NCBI
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Representative proteomes NCBI

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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.

Representative proteomes NCBI
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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...


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_6419 (release 26.0)
Previous IDs: none
Type: Family
Author: Wood V, Coggill P
Number in seed: 51
Number in full: 19474
Average length of the domain: 128.40 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 52.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 35.0 35.0
Trusted cut-off 35.0 35.0
Noise cut-off 34.9 34.9
Model length: 130
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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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The tree shows the occurrence of this domain across different species. More...


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There are 2 interactions for this family. More...

Ribonucleas_3_3 dsrm


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 Ribonucleas_3_3 domain has been found. There are 5 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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