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11  structures 766  species 0  interactions 840  sequences 14  architectures

Family: Rpp20 (PF12328)

Summary: Rpp20 subunit of nuclear RNase MRP and P

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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.

Rpp20 subunit of nuclear RNase MRP and P Provide feedback

The nuclear RNase P of Saccharomyces cerevisiae is made up of at least nine protein subunits; Pop1, Pop3, Pop4, Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these subunits seem to be present also in the RNase MRP, with the exception of Rpr2 (Rpp21) which is unique to RNase P. Human nuclear RNase P and MRP appear to contain at least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25, Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although there is recent evidence that not all of these subunits are shared between P and MRP. Archaeal RNase P has at least four protein subunits homologous to eukaryotic RNase P/MRP proteins [2]. In the yeast RNase P, Pop6 and Pop7 (the Rpp20 homologue) interact with each other and they are both interaction partners of Pop4 [4]; in the human MRP Rpp25 and Rpp20 interact with each other [2] and Rpp25 binds to Rpp29 (Pop4) [3].

Literature references

  1. Stolc V, Katz A, Altman S;, Proc Natl Acad Sci U S A. 1998;95:6716-6721.: Rpp2, an essential protein subunit of nuclear RNase P, is required for processing of precursor tRNAs and 35S precursor rRNA in Saccharomyces cerevisiae. PUBMED:9618478 EPMC:9618478

  2. Welting TJ, van Venrooij WJ, Pruijn GJ;, Nucleic Acids Res. 2004;32:2138-2146.: Mutual interactions between subunits of the human RNase MRP ribonucleoprotein complex. PUBMED:15096576 EPMC:15096576

  3. Rosenblad MA, Lopez MD, Piccinelli P, Samuelsson T;, Nucleic Acids Res. 2006;34:5145-5156.: Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. PUBMED:16998185 EPMC:16998185

  4. Perederina A, Esakova O, Koc H, Schmitt ME, Krasilnikov AS;, RNA. 2007;13:1648-1655.: Specific binding of a Pop6/Pop7 heterodimer to the P3 stem of the yeast RNase MRP and RNase P RNAs. PUBMED:17717080 EPMC:17717080

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014612

This entry includes fission yeast ribonucleases P/MRP protein subunit Pop7 and its homologue, Rpp20, from animals. Pop7/Rpp20 is a component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. They are also a component of RNase MRP complex, which cleaves pre-rRNA sequences [ PUBMED:15096576 , PUBMED:21450806 ].

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 AlbA (CL0441), which has the following description:

This is a family of DNA and RNA binding proteins found from archaea to humans.

The clan contains the following 4 members:

Alba AlbA_2 Rpp20 SpoVS


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 and the UniProtKB 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 UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Representative proteomes UniProt

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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.

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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...


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_33537 (release 23.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Coggill P
Number in seed: 39
Number in full: 840
Average length of the domain: 126.3 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 64.96 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.6 24.6
Trusted cut-off 24.6 24.6
Noise cut-off 24.5 24.5
Model length: 137
Family (HMM) version: 11
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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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 Rpp20 domain has been found. There are 11 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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