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551  structures 8825  species 0  interactions 12238  sequences 86  architectures

Family: Ribosomal_L11_N (PF03946)

Summary: Ribosomal protein L11, N-terminal domain

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Ribosomal protein L11, N-terminal domain Provide feedback

The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020784

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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA and plays a significant role during initiation, elongation, and termination of protein synthesis. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [ PUBMED:2167467 ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. L11 consists of a 23S rRNA binding C-terminal domain and an N-terminal domain that directly contacts protein synthesis factors. These two domains are joined by a flexible linker that allows inter-domain movement during protein synthesis. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA [ PUBMED:18406324 , PUBMED:10338213 , PUBMED:17215866 , PUBMED:18611379 ]. In E. coli, the C-terminal half of L11 has been shown [ PUBMED:2483975 ] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.

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.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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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: L11;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 250
Number in full: 12238
Average length of the domain: 57.9 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 35.42 %

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 32.9 32.9
Trusted cut-off 32.9 32.9
Noise cut-off 32.8 32.8
Model length: 58
Family (HMM) version: 17
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_L11_N domain has been found. There are 551 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
A0A044UYU2 View 3D Structure Click here
A0A044V5M8 View 3D Structure Click here
A0A077ZB50 View 3D Structure Click here
A0A077ZH59 View 3D Structure Click here
A0A077ZKU5 View 3D Structure Click here
A0A0A2V518 View 3D Structure Click here
A0A0D2EKW5 View 3D Structure Click here
A0A0D2GLR1 View 3D Structure Click here
A0A0H3GGN5 View 3D Structure Click here
A0A0K0DUX7 View 3D Structure Click here
A0A0K0E113 View 3D Structure Click here
A0A0K0EJN7 View 3D Structure Click here
A0A0K0J2W6 View 3D Structure Click here
A0A0N4UJ04 View 3D Structure Click here
A0A0P0VSE5 View 3D Structure Click here
A0A0R0EV33 View 3D Structure Click here
A0A0R0GRR3 View 3D Structure Click here
A0A0R0HHB6 View 3D Structure Click here
A0A0R4J4M9 View 3D Structure Click here
A0A175W4X8 View 3D Structure Click here
A0A175WEU9 View 3D Structure Click here
A0A1C1C776 View 3D Structure Click here
A0A1C1CH01 View 3D Structure Click here
A0A1D6KIE7 View 3D Structure Click here
A0A1I9G4B5 View 3D Structure Click here
A0A2R8Q7N4 View 3D Structure Click here
A0A3P7DWY8 View 3D Structure Click here
A0A3P7FN15 View 3D Structure Click here
A0A5K4FB69 View 3D Structure Click here
A0A5S6PDH6 View 3D Structure Click here
A0B923 View 3D Structure Click here
A0JZA3 View 3D Structure Click here
A0KQA9 View 3D Structure Click here
A0L5W2 View 3D Structure Click here
A0LII0 View 3D Structure Click here
A0LRK9 View 3D Structure Click here
A0PXT4 View 3D Structure Click here
A0QS45 View 3D Structure Click here
A0T0C2 View 3D Structure Click here
A0T0Q5 View 3D Structure Click here