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1297  structures 8851  species 0  interactions 12307  sequences 113  architectures

Family: Ribosomal_S11 (PF00411)

Summary: Ribosomal protein S11

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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 S11 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001971

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 S11 [ PUBMED:3191988 ] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. S14 is the eukaryotic homologue of S11; they constitute the uS11 family that includes bacterial, archaeal and eukaryotic proteins [ PUBMED:14568531 ].

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.

Representative proteomes UniProt
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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

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: S11;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 7
Number in full: 12307
Average length of the domain: 109.6 aa
Average identity of full alignment: 51 %
Average coverage of the sequence by the domain: 73.32 %

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 25.1 25.1
Trusted cut-off 25.1 25.1
Noise cut-off 25.0 25.0
Model length: 110
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


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...

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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_S11 domain has been found. There are 1297 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
A0A044UJC9 View 3D Structure Click here
A0A044UWM6 View 3D Structure Click here
A0A077YZK6 View 3D Structure Click here
A0A077ZBT6 View 3D Structure Click here
A0A077ZJB5 View 3D Structure Click here
A0A0D2GW10 View 3D Structure Click here
A0A0H3H3V1 View 3D Structure Click here
A0A0K0DVK8 View 3D Structure Click here
A0A0K0E9U1 View 3D Structure Click here
A0A0N4UMW8 View 3D Structure Click here
A0A0N4UQV3 View 3D Structure Click here
A0A0R0FZ23 View 3D Structure Click here
A0A0R0G495 View 3D Structure Click here
A0A0R0KP31 View 3D Structure Click here
A0A175VV65 View 3D Structure Click here
A0A175WEM0 View 3D Structure Click here
A0A1C1CRT8 View 3D Structure Click here
A0A1D6LPG1 View 3D Structure Click here
A0A1D6QHR9 View 3D Structure Click here
A0A1D8PDT3 View 3D Structure Click here
A0A1S0QIB0 View 3D Structure Click here
A0A1X7YEX2 View 3D Structure Click here
A0A1X7YF18 View 3D Structure Click here
A0A3P7DBP3 View 3D Structure Click here
A0A3P7FLI6 View 3D Structure Click here
A0A5K1K925 View 3D Structure Click here
A0B9L3 View 3D Structure Click here
A0JZ50 View 3D Structure Click here
A0KF43 View 3D Structure Click here
A0L5Z6 View 3D Structure Click here
A0LIL5 View 3D Structure Click here
A0LRP6 View 3D Structure Click here
A0PXX3 View 3D Structure Click here
A0QSL6 View 3D Structure Click here
A0RWI9 View 3D Structure Click here
A0T0J9 View 3D Structure Click here
A0T0Z3 View 3D Structure Click here
A1A094 View 3D Structure Click here
A1ALW5 View 3D Structure Click here
A1AVM3 View 3D Structure Click here