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1180  structures 8590  species 0  interactions 11314  sequences 82  architectures

Family: Ribosomal_L2 (PF00181)

Summary: Ribosomal Proteins L2, RNA binding domain

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Ribosomal Proteins L2, RNA binding domain Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022666

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 L2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [ PUBMED:1579444 ], groups:

  • Eubacterial L2.
  • Algal and plant chloroplast L2.
  • Cyanelle L2.
  • Archaebacterial L2.
  • Plant L2.
  • Slime mold L2.
  • Marchantia polymorpha mitochondrial L2.
  • Paramecium tetraurelia mitochondrial L2.
  • Fission yeast K5, K37 and KD4.
  • Yeast YL6.
  • Vertebrate L8.

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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Alignments

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.

  Seed
(26)
Full
(11314)
Representative proteomes UniProt
(55252)
RP15
(1803)
RP35
(5601)
RP55
(10778)
RP75
(17361)
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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

  Seed
(26)
Full
(11314)
Representative proteomes UniProt
(55252)
RP15
(1803)
RP35
(5601)
RP55
(10778)
RP75
(17361)
Alignment:
Format:
Order:
Sequence:
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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.

  Seed
(26)
Full
(11314)
Representative proteomes UniProt
(55252)
RP15
(1803)
RP35
(5601)
RP55
(10778)
RP75
(17361)
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...

Trees

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: L2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 26
Number in full: 11314
Average length of the domain: 77.20 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 27.07 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.5 27.5
Trusted cut-off 27.5 27.5
Noise cut-off 27.4 27.4
Model length: 77
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Structures

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_L2 domain has been found. There are 1180 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
A0A0N7KRK6 View 3D Structure Click here
A0A0R0J7Z4 View 3D Structure Click here
A0A1D8PF08 View 3D Structure Click here
A0A2P2CLG6 View 3D Structure Click here
A0A3B6UA81 View 3D Structure Click here
A4I8K8 View 3D Structure Click here
B4F9R4 View 3D Structure Click here
B6TGT0 View 3D Structure Click here
D4A6W6 View 3D Structure Click here
E7F8R3 View 3D Structure Click here
F4IMC7 View 3D Structure Click here
I1J8M4 View 3D Structure Click here
I1LI06 View 3D Structure Click here
I1MN72 View 3D Structure Click here
K7LAX9 View 3D Structure Click here
K7LI06 View 3D Structure Click here
O45110 View 3D Structure Click here
P0C497 View 3D Structure Click here
P0CT70 View 3D Structure Click here
P0CT71 View 3D Structure Click here
P0CT72 View 3D Structure Click here
P0CX45 View 3D Structure Click here
P0CX46 View 3D Structure Click here
P13023 View 3D Structure Click here
P17788 View 3D Structure Click here
P18663 View 3D Structure Click here
P32611 View 3D Structure Click here
P46286 View 3D Structure Click here
P54017 View 3D Structure Click here
P56791 View 3D Structure Click here
P60422 View 3D Structure Click here
P60430 View 3D Structure Click here
P62917 View 3D Structure Click here
P62918 View 3D Structure Click here
P62919 View 3D Structure Click here
P92812 View 3D Structure Click here
P93311 View 3D Structure Click here
P9WHA5 View 3D Structure Click here
Q23888 View 3D Structure Click here
Q25807 View 3D Structure Click here
Q2PMM3 View 3D Structure Click here
Q2QNF3 View 3D Structure Click here
Q42064 View 3D Structure Click here
Q498T4 View 3D Structure Click here
Q4D5K2 View 3D Structure Click here
Q4DPQ8 View 3D Structure Click here
Q4PSL7 View 3D Structure Click here
Q5A7P6 View 3D Structure Click here
Q5T653 View 3D Structure Click here
Q6P0V6 View 3D Structure Click here
Q8I3T9 View 3D Structure Click here
Q8II37 View 3D Structure Click here
Q8VZZ8 View 3D Structure Click here
Q9D773 View 3D Structure Click here
Q9V3G1 View 3D Structure Click here
Q9VTF8 View 3D Structure Click here
Q9XVF7 View 3D Structure Click here
Q9Y7P4 View 3D Structure Click here