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416  structures 1786  species 0  interactions 3189  sequences 50  architectures

Family: Ribosomal_L5e (PF17144)

Summary: Ribosomal large subunit proteins 60S L5, and 50S L18

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Ribosomal large subunit proteins 60S L5, and 50S L18 Provide feedback

This family contains the large 60S ribosomal L5 proteins from Eukaryota and the 50S L18 proteins from Archaea. It has been shown that the amino terminal 93 amino acids of P09895 are necessary and sufficient to bind 5S rRNA in vitro [1] suggesting that the entire family has a function in rRNA binding [2,3,4,5].

Literature references

  1. Michael WM, Dreyfuss G; , J Biol Chem 1996;271:11571-11574.: Distinct domains in ribosomal protein L5 mediate 5 S rRNA binding and nucleolar localization. PUBMED:8626719 EPMC:8626719

  2. Furumoto H, Taguchi A, Itoh T, Morinaga T, Itoh T;, FEBS Lett. 2000;486:195-199.: 5S rRNA binding proteins from the hyperthermophilic archaeon, Pyrococcus furiosus. PUBMED:11119702 EPMC:11119702

  3. Barakat A, Szick-Miranda K, Chang IF, Guyot R, Blanc G, Cooke R, Delseny M, Bailey-Serres J;, Plant Physiol. 2001;127:398-415.: The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. PUBMED:11598216 EPMC:11598216

  4. Kressler D, Bange G, Ogawa Y, Stjepanovic G, Bradatsch B, Pratte D, Amlacher S, Strauss D, Yoneda Y, Katahira J, Sinning I, Hurt E;, Science. 2012;338:666-671.: Synchronizing nuclear import of ribosomal proteins with ribosome assembly. PUBMED:23118189 EPMC:23118189

  5. Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN, Beckmann R;, Nature. 2013;497:80-85.: Structures of the human and Drosophila 80S ribosome. PUBMED:23636399 EPMC:23636399

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005485

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 ].

This family consists of ribosomal protein L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits [ PUBMED:8474444 ]. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA [ PUBMED:8219074 ]. This family also includes ribosomal proteins L18 from archaea.

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 S11_L18p (CL0267), which has the following description:

This superfamily includes two ribosomal proteins S11 and L18p as well as a domain from eukaryotic peptide chain release factor. This superfamily is likely to share an RNA-binding function.

The clan contains the following 17 members:

acVLRF1 baeRF_family10 baeRF_family11 baeRF_family12 baeRF_family2 baeRF_family3 baeRF_family5 baeRF_family6 baeRF_family7 baeRF_family8 bVLRF1 eRF1_1 eRF1_2 Host_attach Ribosomal_L18p Ribosomal_L5e Ribosomal_S11


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.

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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: phmmer:P09895
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 94
Number in full: 3189
Average length of the domain: 137.50 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 52.40 %

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 27.0 27.0
Trusted cut-off 27.8 27.1
Noise cut-off 26.5 26.9
Model length: 163
Family (HMM) version: 7
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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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_L5e domain has been found. There are 416 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
A0A0R0KPK5 View 3D Structure Click here
A0A1D6JMR7 View 3D Structure Click here
A0A1D6N4X3 View 3D Structure Click here
A0A368UIG9 View 3D Structure Click here
A0B9V1 View 3D Structure Click here
A1RWR7 View 3D Structure Click here
A2BMD8 View 3D Structure Click here
A2SPM1 View 3D Structure Click here
A2WXX3 View 3D Structure Click here
A3DNC6 View 3D Structure Click here
A4IB88 View 3D Structure Click here
A4YCY5 View 3D Structure Click here
A6UWV7 View 3D Structure Click here
A7I5Q8 View 3D Structure Click here
A8AC01 View 3D Structure Click here
A8M9I3 View 3D Structure Click here
B1L785 View 3D Structure Click here
B8D5V1 View 3D Structure Click here
B8GKF2 View 3D Structure Click here
C4JA45 View 3D Structure Click here
C6A179 View 3D Structure Click here
D3ZHP8 View 3D Structure Click here
I1KHZ4 View 3D Structure Click here
I1KHZ6 View 3D Structure Click here
I1M3C1 View 3D Structure Click here
I1M3C3 View 3D Structure Click here
I1MKN3 View 3D Structure Click here
O05640 View 3D Structure Click here
O26130 View 3D Structure Click here
O28373 View 3D Structure Click here
O44248 View 3D Structure Click here
O59953 View 3D Structure Click here
O74306 View 3D Structure Click here
O76190 View 3D Structure Click here
P09895 View 3D Structure Click here
P14123 View 3D Structure Click here
P22451 View 3D Structure Click here
P26321 View 3D Structure Click here
P46777 View 3D Structure Click here
P47962 View 3D Structure Click here