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UniProtKB - Q9RXK1 (RL4_DEIRA)

Entry version 118 (16 Oct 2019)
Sequence version 3 (23 Jan 2007)
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Protein

50S ribosomal protein L4

Gene

rplD

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).By similarity
Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.
This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
50S ribosomal protein L4
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rplD
Ordered Locus Names:DR_0312
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri243230 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Deinococcus-Thermus › Deinococci › Deinococcales › Deinococcaceae › Deinococcus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002524 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome I

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Complete GO annotation on QuickGO ...

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001292142 – 20550S ribosomal protein L4Add BLAST204

Proteomic databases

PRoteomics IDEntifications database

More...PRIDEi		Q9RXK1

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Part of the 50S ribosomal subunit. Contacts proteins L15 and L34.

6 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		243230.DR_0312

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1205
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		Q9RXK1

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		Q9RXK1

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the universal ribosomal protein uL4 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4106U5A Bacteria
COG0088 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000248767

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q9RXK1

KEGG Orthology (KO)

More...KOi		K02926

Identification of Orthologs from Complete Genome Data

More...OMAi		PQVHILE

Database of Orthologous Groups

More...OrthoDBi		1572673at2

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.40.1370.10, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01328_B Ribosomal_L4_B, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR002136 Ribosomal_L4/L1e
IPR023574 Ribosomal_L4_dom_sf
IPR013005 Ribosomal_uL4/L1e

The PANTHER Classification System

More...PANTHERi		PTHR10746 PTHR10746, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00573 Ribosomal_L4, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52166 SSF52166, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR03953 rplD_bact, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q9RXK1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAQINVIGQN GGRTIELPLP EVNSGVLHEV VTWQLASRRR GTASTRTRAQ 
        60         70         80         90        100
VSKTGRKMYG QKGTGNARHG DRSVPTFVGG GVAFGPKPRS YDYTLPRQVR 
       110        120        130        140        150
QLGLAMAIAS RQEGGKLVAV DGFDIADAKT KNFISWAKQN GLDGTEKVLL 
       160        170        180        190        200
VTDDENTRRA ARNVSWVSVL PVAGVNVYDI LRHDRLVIDA AALEIVEEEA 

GEEQQ
Length:205
Mass (Da):22,278
Last modified:January 23, 2007 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i760A6C160912477B
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
AE000513 Genomic DNA Translation: AAF09893.1

Protein sequence database of the Protein Information Resource

More...PIRi		H75533

NCBI Reference Sequences

More...RefSeqi		NP_294035.1, NC_001263.1
WP_010886957.1, NZ_CP015081.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAF09893; AAF09893; DR_0312

Database of genes from NCBI RefSeq genomes

More...GeneIDi		1799571

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		dra:DR_0312

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|243230.17.peg.478

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA Translation: AAF09893.1
PIRiH75533
RefSeqiNP_294035.1, NC_001263.1
WP_010886957.1, NZ_CP015081.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1J5AX-ray3.50K1-205[»]
1JZXX-ray3.10K1-205[»]
1JZYX-ray3.50K1-205[»]
1JZZX-ray3.80K1-205[»]
1K01X-ray3.50K1-205[»]
1NKWX-ray3.10C1-205[»]
1NWXX-ray3.50C2-205[»]
1NWYX-ray3.30C2-205[»]
1SM1X-ray3.42C1-205[»]
1XBPX-ray3.50C2-205[»]
2ZJPX-ray3.70C1-205[»]
2ZJQX-ray3.30C1-205[»]
2ZJRX-ray2.91C1-205[»]
3CF5X-ray3.30C1-205[»]
3DLLX-ray3.50C1-205[»]
3PIOX-ray3.25C1-205[»]
3PIPX-ray3.45C1-205[»]
4IO9X-ray3.20C1-205[»]
4IOAX-ray3.20C1-205[»]
4IOCX-ray3.60C1-205[»]
4U67X-ray3.65C1-205[»]
4V49X-ray8.70C2-198[»]
4V4AX-ray9.50C2-198[»]
4WFNX-ray3.54C1-205[»]
5DM6X-ray2.90C2-198[»]
5DM7X-ray3.00C2-198[»]
5JVGX-ray3.43C1-205[»]
5JVHX-ray3.58C1-205[»]
SMRiQ9RXK1
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0312

Proteomic databases

PRIDEiQ9RXK1

Genome annotation databases

EnsemblBacteriaiAAF09893; AAF09893; DR_0312
GeneIDi1799571
KEGGidra:DR_0312
PATRICifig|243230.17.peg.478

Phylogenomic databases

eggNOGiENOG4106U5A Bacteria
COG0088 LUCA
HOGENOMiHOG000248767
InParanoidiQ9RXK1
KOiK02926
OMAiPQVHILE
OrthoDBi1572673at2

Miscellaneous databases

EvolutionaryTraceiQ9RXK1

Family and domain databases

Gene3Di3.40.1370.10, 1 hit
HAMAPiMF_01328_B Ribosomal_L4_B, 1 hit
InterProiView protein in InterPro
IPR002136 Ribosomal_L4/L1e
IPR023574 Ribosomal_L4_dom_sf
IPR013005 Ribosomal_uL4/L1e
PANTHERiPTHR10746 PTHR10746, 1 hit
PfamiView protein in Pfam
PF00573 Ribosomal_L4, 1 hit
SUPFAMiSSF52166 SSF52166, 1 hit
TIGRFAMsiTIGR03953 rplD_bact, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRL4_DEIRA
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9RXK1
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: January 23, 2007
Last modified: October 16, 2019
This is version 118 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Ribosomal proteins
    Ribosomal proteins families and list of entries
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