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UniProtKB - P42921 (RL4_BACSU)

Entry version 131 (23 Feb 2022)
Sequence version 1 (01 Nov 1995)
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Protein

50S ribosomal protein L4

Gene

rplD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:3 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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.

UniRule annotation

Forms part of the polypeptide exit tunnel.

UniRule annotation

<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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU01170-MONOMER

<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%5Fand%5Ftaxonomy%5Fsection">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 L4UniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:rplDUniRule annotation
Ordered Locus Names:BSU01170
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

<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

<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 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001291831 – 20750S ribosomal protein L4Add BLAST207

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P42921

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P42921

PRoteomics IDEntifications database

More...PRIDEi		P42921

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Part of the 50S ribosomal subunit.

1 Publication

Protein-protein interaction databases

Protein interaction database and analysis system

More...IntActi		P42921, 1 interactor

STRING: functional protein association networks

More...STRINGi		224308.BSU01170

<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

1207
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		P42921

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni48 – 85DisorderedSequence analysisAdd BLAST38

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi49 – 63Basic and acidic residuesSequence analysisAdd BLAST15

<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.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0088, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P42921

Identification of Orthologs from Complete Genome Data

More...OMAi		PQVHILE

Database for complete collections of gene phylogenies

More...PhylomeDBi		P42921

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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P42921-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK 
        60         70         80         90        100
VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVVF GPTPRSYSYK 
       110        120        130        140        150
LPKKVRRLAI KSVLSSKVID NNIIVLEDLT LDTAKTKEMA AILKGLSVEK 
       160        170        180        190        200
KALIVTADAN EAVALSARNI PGVTVVEANG INVLDVVNHE KLLITKAAVE 

KVEEVLA
Length:207
Mass (Da):22,391
Last modified:November 1, 1995 - v1
<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:iBF9DAD4CFA66725C
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
U43929 Genomic DNA Translation: AAC45957.1
D50302 Genomic DNA Translation: BAA08832.1
AL009126 Genomic DNA Translation: CAB11893.1

Protein sequence database of the Protein Information Resource

More...PIRi		H69694

NCBI Reference Sequences

More...RefSeqi		NP_387998.1, NC_000964.3
WP_004399658.1, NZ_JNCM01000029.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB11893; CAB11893; BSU_01170

Database of genes from NCBI RefSeq genomes

More...GeneIDi		936690

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU01170

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.120

<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
U43929 Genomic DNA Translation: AAC45957.1
D50302 Genomic DNA Translation: BAA08832.1
AL009126 Genomic DNA Translation: CAB11893.1
PIRiH69694
RefSeqiNP_387998.1, NC_000964.3
WP_004399658.1, NZ_JNCM01000029.1

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
3J3Velectron microscopy13.30E1-207[»]
3J3Welectron microscopy10.70E1-207[»]
3J9Welectron microscopy3.90BF1-207[»]
5NJTelectron microscopy3.80Y2-206[»]
6HA1electron microscopy3.10E1-207[»]
6HA8electron microscopy3.50E1-207[»]
6HTQelectron microscopy4.50E2-206[»]
6PPFelectron microscopy3.40E1-207[»]
6PPKelectron microscopy4.40E1-207[»]
6PVKelectron microscopy3.40E1-207[»]
6TNNelectron microscopy3.07Y1-207[»]
6TPQelectron microscopy3.07Y1-207[»]
7AQCelectron microscopy2.99E1-207[»]
7AQDelectron microscopy3.10E1-207[»]
7AS8electron microscopy2.90G1-207[»]
7AS9electron microscopy3.50G1-207[»]
7OPEelectron microscopy3.20G1-207[»]
SMRiP42921
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

IntActiP42921, 1 interactor
STRINGi224308.BSU01170

Proteomic databases

jPOSTiP42921
PaxDbiP42921
PRIDEiP42921

Genome annotation databases

EnsemblBacteriaiCAB11893; CAB11893; BSU_01170
GeneIDi936690
KEGGibsu:BSU01170
PATRICifig|224308.179.peg.120

Phylogenomic databases

eggNOGiCOG0088, Bacteria
InParanoidiP42921
OMAiPQVHILE
PhylomeDBiP42921

Enzyme and pathway databases

BioCyciBSUB:BSU01170-MONOMER

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

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_BACSU
<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: P42921
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: February 23, 2022
This is version 131 of the entry and version 1 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, Reference proteome

Documents

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