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1320  structures 8853  species 0  interactions 12215  sequences 88  architectures

Family: Ribosom_S12_S23 (PF00164)

Summary: Ribosomal protein S12/S23

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Ribosomal protein S12/S23 Provide feedback

This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006032

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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea.

Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.

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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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: Prosite
Previous IDs: S12; Ribosomal_S12;
Type: Family
Sequence Ontology: SO:0100021
Author: Sonnhammer ELL
Number in seed: 12
Number in full: 12215
Average length of the domain: 110.20 aa
Average identity of full alignment: 55 %
Average coverage of the sequence by the domain: 78.65 %

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 22.3 22.3
Trusted cut-off 22.4 22.8
Noise cut-off 22.2 22.2
Model length: 114
Family (HMM) version: 28
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 Ribosom_S12_S23 domain has been found. There are 1320 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
A0A0P0VA20 View 3D Structure Click here
A0A0P0XT53 View 3D Structure Click here
A0A0P0XTN9 View 3D Structure Click here
A0A0R0H296 View 3D Structure Click here
A0A0R0I4C0 View 3D Structure Click here
A0A0R0JLD5 View 3D Structure Click here
A0A1D6EFR3 View 3D Structure Click here
A0A1D6HTP3 View 3D Structure Click here
A0A1D6JSB4 View 3D Structure Click here
A0A1D6LL85 View 3D Structure Click here
A0A1D6NL33 View 3D Structure Click here
A0A1D6PHK8 View 3D Structure Click here
A0A1D8PDU3 View 3D Structure Click here
A0A2P2CLH1 View 3D Structure Click here
A0A3B6UD92 View 3D Structure Click here
A8KB78 View 3D Structure Click here
B4FBY5 View 3D Structure Click here
D3ZMK3 View 3D Structure Click here
D3ZQX3 View 3D Structure Click here
D4A9Q3 View 3D Structure Click here
E7F8G8 View 3D Structure Click here
E9AGX4 View 3D Structure Click here
F1LTW8 View 3D Structure Click here
I1L8S1 View 3D Structure Click here
I1LZ09 View 3D Structure Click here
K7K214 View 3D Structure Click here
M1FIQ5 View 3D Structure Click here
O14182 View 3D Structure Click here
O15235 View 3D Structure Click here
O35680 View 3D Structure Click here
O97248 View 3D Structure Click here
P07134 View 3D Structure Click here
P0A0H0 View 3D Structure Click here
P0A7S3 View 3D Structure Click here
P0CT75 View 3D Structure Click here
P0CT76 View 3D Structure Click here
P0CX29 View 3D Structure Click here
P0CX30 View 3D Structure Click here
P10735 View 3D Structure Click here
P12149 View 3D Structure Click here