Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
1357  structures 8855  species 0  interactions 13656  sequences 102  architectures

Family: Ribosomal_L3 (PF00297)

Summary: Ribosomal protein L3

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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 L3 Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000597

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 L3 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities includes bacterial, red algal, cyanelle, mammalian, yeast and Arabidopsis thaliana L3 proteins; archaeal Haloarcula marismortui HmaL3 (HL1), and yeast mitochondrial YmL9 [ PUBMED:1597181 , PUBMED:1499563 , PUBMED:2406244 ].

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan EFTPs (CL0575), which has the following description:

This superfamily is characterised ba a barrel that is formed as a greek-key. It is found as the second domain in many elongation factor proteins, as well as in an elaborated from in two ribosomal proteins and in some other N-terminal domains, eg of AlaX and Gar1 and RimM protein famlies.

The clan contains the following 7 members:

Gar1 GTP_EFTU_D2 NSP2_assoc RIBIOP_C Ribosomal_L3 Ribosomal_L35Ae RimM


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...

View options

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
Jalview View  View  View  View  View  View  View 
HTML View             
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
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: L3;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 7
Number in full: 13656
Average length of the domain: 171.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 64.49 %

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 22.8 22.8
Trusted cut-off 22.8 22.9
Noise cut-off 22.6 22.7
Model length: 369
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


Align selected sequences to HMM

Generate a FASTA-format file

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...

Loading sunburst data...

Tree controls


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


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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_L3 domain has been found. There are 1357 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.

Loading structure mapping...

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
A0A0R4IY00 View 3D Structure Click here
A0A1D6E101 View 3D Structure Click here
A0A1D6EAY0 View 3D Structure Click here
A0A1D6QLP3 View 3D Structure Click here
A0A1D8PRP6 View 3D Structure Click here
A0A368UIA2 View 3D Structure Click here
A0B9X0 View 3D Structure Click here
A0JZ84 View 3D Structure Click here
A0KF21 View 3D Structure Click here
A0L5X3 View 3D Structure Click here
A0LIJ0 View 3D Structure Click here
A0LRM0 View 3D Structure Click here
A0PXU6 View 3D Structure Click here
A0QSD1 View 3D Structure Click here
A0T0H8 View 3D Structure Click here
A0T0X2 View 3D Structure Click here
A1A069 View 3D Structure Click here
A1ALU1 View 3D Structure Click here
A1AVK0 View 3D Structure Click here
A1B027 View 3D Structure Click here
A1BJ34 View 3D Structure Click here
A1KB27 View 3D Structure Click here
A1R8U5 View 3D Structure Click here
A1S218 View 3D Structure Click here
A1SNL8 View 3D Structure Click here
A1T0E2 View 3D Structure Click here
A1T4N9 View 3D Structure Click here
A1TJ07 View 3D Structure Click here
A1UBN6 View 3D Structure Click here
A1USL4 View 3D Structure Click here
A1VIQ0 View 3D Structure Click here
A1W2Q7 View 3D Structure Click here
A1WHC5 View 3D Structure Click here
A1WVC2 View 3D Structure Click here
A2SLF7 View 3D Structure Click here
A2SPK3 View 3D Structure Click here
A3A2Y2 View 3D Structure Click here
A3CK63 View 3D Structure Click here
A3DJH2 View 3D Structure Click here
A3DNA4 View 3D Structure Click here