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1327  structures 8845  species 0  interactions 12015  sequences 85  architectures

Family: Ribosomal_S15 (PF00312)

Summary: Ribosomal protein S15

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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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.

Ribosomal protein S15 Provide feedback

No Pfam abstract.

Literature references

  1. Clemons WM Jr, Davies C, White SW, Ramakrishnan V; , Structure 1998;6:429-438.: Conformational variability of the N-terminal helix in the structure of ribosomal protein S15. PUBMED:9562554 EPMC:9562554

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000589

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [ PUBMED:11297922 , PUBMED:11290319 ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ PUBMED:11290319 , PUBMED:11114498 ].

Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [ PUBMED:2263452 ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.

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 S15_NS1 (CL0600), which has the following description:

The clan contains the following 4 members:

Flu_B_NS1 Flu_NS1 Ribosomal_S15 WHEP-TRS


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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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

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.

Representative proteomes UniProt
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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: Prosite
Previous IDs: S15;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 605
Number in full: 12015
Average length of the domain: 80.3 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 59.62 %

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 31.0 31.0
Trusted cut-off 31.3 31.0
Noise cut-off 30.9 30.8
Model length: 81
Family (HMM) version: 25
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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Clear selection

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 Ribosomal_S15 domain has been found. There are 1327 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044UA59 View 3D Structure Click here
A0A077YXH8 View 3D Structure Click here
A0A077ZFK5 View 3D Structure Click here
A0A0D2F9S7 View 3D Structure Click here
A0A0D2FBG4 View 3D Structure Click here
A0A0H3H3H3 View 3D Structure Click here
A0A0I9N9M9 View 3D Structure Click here
A0A0J9XQX2 View 3D Structure Click here
A0A0K0DX23 View 3D Structure Click here
A0A0K0EHJ5 View 3D Structure Click here
A0A0N4UN27 View 3D Structure Click here
A0A0P0WTS1 View 3D Structure Click here
A0A158N8N6 View 3D Structure Click here
A0A175VNG7 View 3D Structure Click here
A0A175W3M8 View 3D Structure Click here
A0A183XDT3 View 3D Structure Click here
A0A1C1CEP2 View 3D Structure Click here
A0A1C1CK75 View 3D Structure Click here
A0A1D6PWX7 View 3D Structure Click here
A0A1D6QBY0 View 3D Structure Click here
A0A1D8PPE0 View 3D Structure Click here
A0A1D8PRY0 View 3D Structure Click here
A0A3B6UDB5 View 3D Structure Click here
A0A5K4F4N4 View 3D Structure Click here
A0A5K4F7E2 View 3D Structure Click here
A0B5E6 View 3D Structure Click here
A0JUV7 View 3D Structure Click here
A0KNE0 View 3D Structure Click here
A0LE15 View 3D Structure Click here
A0LHM3 View 3D Structure Click here
A0LV21 View 3D Structure Click here
A0Q0Q2 View 3D Structure Click here
A0QVQ3 View 3D Structure Click here
A0RTT1 View 3D Structure Click here
A1A007 View 3D Structure Click here
A1AMM5 View 3D Structure Click here
A1AVW6 View 3D Structure Click here
A1B5Q0 View 3D Structure Click here
A1BDF5 View 3D Structure Click here
A1E9X0 View 3D Structure Click here