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928  structures 7801  species 0  interactions 9086  sequences 13  architectures

Family: Ribosomal_L35p (PF01632)

Summary: Ribosomal protein L35

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Ribosomal protein L35 Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021137

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 ].

L35 is a basic protein of 60 to 70 amino-acid residues from the large subunit [ PUBMED:3542048 ]. Like many basic polypeptides, L35 completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes [ PUBMED:3542048 ]. It belongs to a family of ribosomal proteins, including L35 from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants [ PUBMED:2271612 ].

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...

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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.

  Seed
(538)
Full
(9086)
Representative proteomes UniProt
(37744)
RP15
(1411)
RP35
(4596)
RP55
(9209)
RP75
(15371)
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HTML View             
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
(538)
Full
(9086)
Representative proteomes UniProt
(37744)
RP15
(1411)
RP35
(4596)
RP55
(9209)
RP75
(15371)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(538)
Full
(9086)
Representative proteomes UniProt
(37744)
RP15
(1411)
RP35
(4596)
RP55
(9209)
RP75
(15371)
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: Pfam-B_1156 (release 4.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 538
Number in full: 9086
Average length of the domain: 60.70 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 76.86 %

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 28.9 28.9
Trusted cut-off 28.9 28.9
Noise cut-off 28.8 28.7
Model length: 61
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

Selections

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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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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_L35p domain has been found. There are 928 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
A0A0P0XYA1 View 3D Structure Click here
A0A0R0IB98 View 3D Structure Click here
A0A1D6KA90 View 3D Structure Click here
A0A1D8PCD7 View 3D Structure Click here
A0JV02 View 3D Structure Click here
A0KKP7 View 3D Structure Click here
A0L4J8 View 3D Structure Click here
A0LFC4 View 3D Structure Click here
A0LUD0 View 3D Structure Click here
A0PZN3 View 3D Structure Click here
A0QYU7 View 3D Structure Click here
A0T0F5 View 3D Structure Click here
A0T0Q1 View 3D Structure Click here
A1A2C3 View 3D Structure Click here
A1ARE3 View 3D Structure Click here
A1B4C2 View 3D Structure Click here
A1BJB4 View 3D Structure Click here
A1K4E3 View 3D Structure Click here
A1R567 View 3D Structure Click here
A1S6G6 View 3D Structure Click here
A1SJH9 View 3D Structure Click here
A1TAC4 View 3D Structure Click here
A1TR37 View 3D Structure Click here
A1UHB0 View 3D Structure Click here
A1UUB0 View 3D Structure Click here
A1VR75 View 3D Structure Click here
A1W8I4 View 3D Structure Click here
A1WMG7 View 3D Structure Click here
A1WU55 View 3D Structure Click here
A2SH05 View 3D Structure Click here
A3CNY8 View 3D Structure Click here
A3DES7 View 3D Structure Click here
A3MYU6 View 3D Structure Click here
A3PFE9 View 3D Structure Click here
A3QEJ8 View 3D Structure Click here
A4FKE4 View 3D Structure Click here
A4G617 View 3D Structure Click here
A4J4Y9 View 3D Structure Click here
A4SCK2 View 3D Structure Click here
A4VM20 View 3D Structure Click here