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338  structures 1759  species 0  interactions 2891  sequences 48  architectures

Family: Ribosomal_L31e (PF01198)

Summary: Ribosomal protein L31e

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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 L31e Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000054

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 ].

A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of:

Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit [ PUBMED:12554856 , PUBMED:10937990 , PUBMED:12007402 , PUBMED:11909526 , PUBMED:11904172 , PUBMED:11114498 , PUBMED:11297922 , PUBMED:7711082 , PUBMED:9657144 , PUBMED:11598216 , PUBMED:14976550 , PUBMED:18400176 , PUBMED:2597680 , PUBMED:8722009 , PUBMED:10937989 , PUBMED:11875025 , PUBMED:14561884 , PUBMED:15189156 , PUBMED:15334087 ].

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

Key: ✓ available, x not generated, not 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.

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: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 82
Number in full: 2891
Average length of the domain: 78.2 aa
Average identity of full alignment: 55 %
Average coverage of the sequence by the domain: 55.04 %

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 25.0 25.0
Trusted cut-off 25.0 25.1
Noise cut-off 24.7 24.9
Model length: 82
Family (HMM) version: 22
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 Ribosomal_L31e domain has been found. There are 338 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
A0A044UN50 View 3D Structure Click here
A0A077YYZ8 View 3D Structure Click here
A0A0D2F449 View 3D Structure Click here
A0A0G2JWD9 View 3D Structure Click here
A0A0G2K7E3 View 3D Structure Click here
A0A0I9N9W2 View 3D Structure Click here
A0A0K0DYW3 View 3D Structure Click here
A0A0N4UH31 View 3D Structure Click here
A0A175WI70 View 3D Structure Click here
A0A1C1CNS2 View 3D Structure Click here
A0A1D8PHF5 View 3D Structure Click here
A2BN56 View 3D Structure Click here
A2STI8 View 3D Structure Click here
A3DNH4 View 3D Structure Click here
A4IBL9 View 3D Structure Click here
A6UT96 View 3D Structure Click here
A7I9I7 View 3D Structure Click here
A8A968 View 3D Structure Click here
B6SJJ1 View 3D Structure Click here
B6SNJ5 View 3D Structure Click here
B6U961 View 3D Structure Click here
B8D5Q6 View 3D Structure Click here
B8GEU5 View 3D Structure Click here
C0NHE0 View 3D Structure Click here
C1H2H2 View 3D Structure Click here
C6SVR2 View 3D Structure Click here
C6SW35 View 3D Structure Click here
C6SYY9 View 3D Structure Click here
D3Z8W1 View 3D Structure Click here
D3ZAC7 View 3D Structure Click here
D3ZDE9 View 3D Structure Click here
D3ZK34 View 3D Structure Click here
D3ZKU5 View 3D Structure Click here
D3ZLA5 View 3D Structure Click here
D3ZU04 View 3D Structure Click here
D3ZVF5 View 3D Structure Click here
D3ZVY6 View 3D Structure Click here
D3ZX87 View 3D Structure Click here
D3ZZ60 View 3D Structure Click here
D4A172 View 3D Structure Click here