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Protein

30S ribosomal protein S13

Gene

rpsM

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.1 Publication
In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.4 Publications
Contacts the tRNAs in the A and P sites.1 Publication
The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding, tRNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10912-MONOMER.
ECOL316407:JW3260-MONOMER.
MetaCyc:EG10912-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
30S ribosomal protein S13
Gene namesi
Name:rpsM
Ordered Locus Names:b3298, JW3260
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10912. rpsM.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • cytosolic small ribosomal subunit Source: EcoliWiki
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi83 – 118Missing : Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro. 1 PublicationAdd BLAST36
Mutagenesisi114 – 118Missing : Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro. 1 Publication5

Chemistry databases

DrugBankiDB00560. Tigecycline.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001320892 – 11830S ribosomal protein S13Add BLAST117

Proteomic databases

EPDiP0A7S9.
PaxDbiP0A7S9.
PRIDEiP0A7S9.

Interactioni

Subunit structurei

Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Cross-links to the P site tRNA and weakly to the A site tRNA. Forms two bridges to the 50S subunit in the 70S ribosome, contacting the 16S rRNA and proteins S19 and L5.

Protein-protein interaction databases

DIPiDIP-35855N.
IntActiP0A7S9. 101 interactors.
MINTiMINT-1290225.
STRINGi511145.b3298.

Structurei

Secondary structure

1118
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 7Combined sources3
Beta strandi12 – 14Combined sources3
Helixi15 – 19Combined sources5
Turni21 – 24Combined sources4
Helixi28 – 36Combined sources9
Beta strandi41 – 43Combined sources3
Beta strandi45 – 47Combined sources3
Helixi50 – 60Combined sources11
Beta strandi61 – 63Combined sources3
Helixi67 – 83Combined sources17
Helixi86 – 92Combined sources7
Turni97 – 99Combined sources3
Beta strandi102 – 104Combined sources3
Helixi107 – 109Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M5Gmodel-M2-118[»]
2YKRelectron microscopy9.80M2-115[»]
3J9Yelectron microscopy3.90m1-118[»]
3J9Zelectron microscopy3.60SM2-118[»]
3JA1electron microscopy3.60SM2-118[»]
3JBUelectron microscopy3.64M1-118[»]
3JBVelectron microscopy3.32M1-118[»]
3JCDelectron microscopy3.70m1-118[»]
3JCEelectron microscopy3.20m1-118[»]
3JCJelectron microscopy3.70s1-118[»]
3JCNelectron microscopy4.60n1-118[»]
4A2Ielectron microscopy16.50M2-115[»]
4ADVelectron microscopy13.50M2-118[»]
4U1UX-ray2.95AM/CM2-115[»]
4U1VX-ray3.00AM/CM2-115[»]
4U20X-ray2.90AM/CM2-115[»]
4U24X-ray2.90AM/CM2-115[»]
4U25X-ray2.90AM/CM2-115[»]
4U26X-ray2.80AM/CM2-115[»]
4U27X-ray2.80AM/CM2-115[»]
4V47electron microscopy12.30BM2-118[»]
4V48electron microscopy11.50BM2-118[»]
4V4HX-ray3.46AM/CM1-118[»]
4V4QX-ray3.46AM/CM2-118[»]
4V4Velectron microscopy15.00AM2-116[»]
4V4Welectron microscopy15.00AM2-116[»]
4V50X-ray3.22AM/CM2-118[»]
4V52X-ray3.21AM/CM2-118[»]
4V53X-ray3.54AM/CM2-118[»]
4V54X-ray3.30AM/CM2-118[»]
4V55X-ray4.00AM/CM2-118[»]
4V56X-ray3.93AM/CM2-118[»]
4V57X-ray3.50AM/CM2-118[»]
4V5BX-ray3.74BM/DM2-118[»]
4V5Helectron microscopy5.80AM2-114[»]
4V5YX-ray4.45AM/CM2-118[»]
4V64X-ray3.50AM/CM2-118[»]
4V65electron microscopy9.00AF1-118[»]
4V66electron microscopy9.00AF1-118[»]
4V69electron microscopy6.70AM2-114[»]
4V6CX-ray3.19AM/CM1-118[»]
4V6DX-ray3.81AM/CM1-118[»]
4V6EX-ray3.71AM/CM1-118[»]
4V6Kelectron microscopy8.25BQ1-118[»]
4V6Lelectron microscopy13.20AQ1-118[»]
4V6Nelectron microscopy12.10BP2-118[»]
4V6Oelectron microscopy14.70AP2-118[»]
4V6Pelectron microscopy13.50AP2-118[»]
4V6Qelectron microscopy11.50AP2-118[»]
4V6Relectron microscopy11.50AP2-118[»]
4V6Selectron microscopy13.10BO2-118[»]
4V6Telectron microscopy8.30AM2-115[»]
4V6Velectron microscopy9.80AM2-118[»]
4V6Yelectron microscopy12.00AM1-114[»]
4V6Zelectron microscopy12.00AM1-114[»]
4V70electron microscopy17.00AM1-114[»]
4V71electron microscopy20.00AM1-114[»]
4V72electron microscopy13.00AM1-114[»]
4V73electron microscopy15.00AM1-114[»]
4V74electron microscopy17.00AM1-114[»]
4V75electron microscopy12.00AM1-114[»]
4V76electron microscopy17.00AM1-114[»]
4V77electron microscopy17.00AM1-114[»]
4V78electron microscopy20.00AM1-114[»]
4V79electron microscopy15.00AM1-114[»]
4V7Aelectron microscopy9.00AM1-114[»]
4V7Belectron microscopy6.80AM1-118[»]
4V7Celectron microscopy7.60AM2-118[»]
4V7Delectron microscopy7.60BM2-118[»]
4V7Ielectron microscopy9.60BM1-118[»]
4V7SX-ray3.25AM2-115[»]
CM2-114[»]
4V7TX-ray3.19AM2-115[»]
CM2-114[»]
4V7UX-ray3.10AM/CM2-115[»]
4V7VX-ray3.29AM2-115[»]
CM2-114[»]
4V85X-ray3.20M1-118[»]
4V89X-ray3.70AM1-118[»]
4V9CX-ray3.30AM/CM1-118[»]
4V9DX-ray3.00AM/BM2-115[»]
4V9OX-ray2.90BM/DM/FM/HM1-118[»]
4V9PX-ray2.90BM/DM/FM/HM1-118[»]
4WF1X-ray3.09AM/CM2-115[»]
4WOIX-ray3.00AM/DM1-118[»]
4WWWX-ray3.10QM/XM2-115[»]
4YBBX-ray2.10AM/BM2-115[»]
5AFIelectron microscopy2.90m1-118[»]
5IQRelectron microscopy3.00r1-118[»]
5IT8X-ray3.12AM/BM2-115[»]
5J5BX-ray2.80AM/BM2-115[»]
5J7LX-ray3.00AM/BM2-115[»]
5J88X-ray3.32AM/BM2-115[»]
5J8AX-ray3.10AM/BM2-115[»]
5J91X-ray2.96AM/BM2-115[»]
5JC9X-ray3.03AM/BM2-115[»]
5JTEelectron microscopy3.60AM1-118[»]
5JU8electron microscopy3.60AM1-118[»]
5KCRelectron microscopy3.601m1-118[»]
5KCSelectron microscopy3.901m1-118[»]
5KPSelectron microscopy3.90181-118[»]
5KPVelectron microscopy4.10171-118[»]
5KPWelectron microscopy3.90171-118[»]
5KPXelectron microscopy3.90171-118[»]
5L3Pelectron microscopy3.70m1-118[»]
ProteinModelPortaliP0A7S9.
SMRiP0A7S9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7S9.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein S13P family.Curated

Phylogenomic databases

eggNOGiENOG4108Z04. Bacteria.
COG0099. LUCA.
HOGENOMiHOG000039879.
InParanoidiP0A7S9.
KOiK02952.
OMAiRTKNNSR.
PhylomeDBiP0A7S9.

Family and domain databases

Gene3Di4.10.910.10. 1 hit.
HAMAPiMF_01315. Ribosomal_S13_S18. 1 hit.
InterProiIPR027437. 30s_Rbsml_prot_S13_C.
IPR001892. Ribosomal_S13.
IPR010979. Ribosomal_S13-like_H2TH.
IPR019980. Ribosomal_S13_bac-type.
IPR018269. Ribosomal_S13_CS.
[Graphical view]
PfamiPF00416. Ribosomal_S13. 1 hit.
[Graphical view]
PIRSFiPIRSF002134. Ribosomal_S13. 1 hit.
SUPFAMiSSF46946. SSF46946. 1 hit.
TIGRFAMsiTIGR03631. uS13_bact. 1 hit.
PROSITEiPS00646. RIBOSOMAL_S13_1. 1 hit.
PS50159. RIBOSOMAL_S13_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A7S9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE
60 70 80 90 100
GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGLR HRRGLPVRGQ
110
RTKTNARTRK GPRKPIKK
Length:118
Mass (Da):13,099
Last modified:January 23, 2007 - v2
Checksum:i6277C365EBE4F732
GO

Mass spectrometryi

Molecular mass is 12968.1 Da from positions 2 - 118. Determined by MALDI. 1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti89 – 99Missing in PW118; partially suppresses a rimM deletion. Add BLAST11
Natural varianti100 – 118Missing in rpsM413; pseudorevertant of streptomycin resistance. A strong antisuppressor of two tRNA suppressors, decreases translation step time and growth rate. Add BLAST19
Natural varianti105N → H in PW095; partially suppresses a rimM deletion. 1
Natural varianti105N → K in PW097; partially suppresses a rimM deletion. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02543 Genomic DNA. Translation: CAA26392.1.
U18997 Genomic DNA. Translation: AAA58093.1.
U00096 Genomic DNA. Translation: AAC76323.1.
AP009048 Genomic DNA. Translation: BAE77993.1.
M12432 Genomic DNA. Translation: AAA83903.1.
M10213 Genomic DNA. Translation: AAA72457.1.
PIRiA23807. R3EC13.
RefSeqiNP_417757.1. NC_000913.3.
WP_000090775.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76323; AAC76323; b3298.
BAE77993; BAE77993; BAE77993.
GeneIDi947791.
KEGGiecj:JW3260.
eco:b3298.
PATRICi32122028. VBIEscCol129921_3391.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02543 Genomic DNA. Translation: CAA26392.1.
U18997 Genomic DNA. Translation: AAA58093.1.
U00096 Genomic DNA. Translation: AAC76323.1.
AP009048 Genomic DNA. Translation: BAE77993.1.
M12432 Genomic DNA. Translation: AAA83903.1.
M10213 Genomic DNA. Translation: AAA72457.1.
PIRiA23807. R3EC13.
RefSeqiNP_417757.1. NC_000913.3.
WP_000090775.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M5Gmodel-M2-118[»]
2YKRelectron microscopy9.80M2-115[»]
3J9Yelectron microscopy3.90m1-118[»]
3J9Zelectron microscopy3.60SM2-118[»]
3JA1electron microscopy3.60SM2-118[»]
3JBUelectron microscopy3.64M1-118[»]
3JBVelectron microscopy3.32M1-118[»]
3JCDelectron microscopy3.70m1-118[»]
3JCEelectron microscopy3.20m1-118[»]
3JCJelectron microscopy3.70s1-118[»]
3JCNelectron microscopy4.60n1-118[»]
4A2Ielectron microscopy16.50M2-115[»]
4ADVelectron microscopy13.50M2-118[»]
4U1UX-ray2.95AM/CM2-115[»]
4U1VX-ray3.00AM/CM2-115[»]
4U20X-ray2.90AM/CM2-115[»]
4U24X-ray2.90AM/CM2-115[»]
4U25X-ray2.90AM/CM2-115[»]
4U26X-ray2.80AM/CM2-115[»]
4U27X-ray2.80AM/CM2-115[»]
4V47electron microscopy12.30BM2-118[»]
4V48electron microscopy11.50BM2-118[»]
4V4HX-ray3.46AM/CM1-118[»]
4V4QX-ray3.46AM/CM2-118[»]
4V4Velectron microscopy15.00AM2-116[»]
4V4Welectron microscopy15.00AM2-116[»]
4V50X-ray3.22AM/CM2-118[»]
4V52X-ray3.21AM/CM2-118[»]
4V53X-ray3.54AM/CM2-118[»]
4V54X-ray3.30AM/CM2-118[»]
4V55X-ray4.00AM/CM2-118[»]
4V56X-ray3.93AM/CM2-118[»]
4V57X-ray3.50AM/CM2-118[»]
4V5BX-ray3.74BM/DM2-118[»]
4V5Helectron microscopy5.80AM2-114[»]
4V5YX-ray4.45AM/CM2-118[»]
4V64X-ray3.50AM/CM2-118[»]
4V65electron microscopy9.00AF1-118[»]
4V66electron microscopy9.00AF1-118[»]
4V69electron microscopy6.70AM2-114[»]
4V6CX-ray3.19AM/CM1-118[»]
4V6DX-ray3.81AM/CM1-118[»]
4V6EX-ray3.71AM/CM1-118[»]
4V6Kelectron microscopy8.25BQ1-118[»]
4V6Lelectron microscopy13.20AQ1-118[»]
4V6Nelectron microscopy12.10BP2-118[»]
4V6Oelectron microscopy14.70AP2-118[»]
4V6Pelectron microscopy13.50AP2-118[»]
4V6Qelectron microscopy11.50AP2-118[»]
4V6Relectron microscopy11.50AP2-118[»]
4V6Selectron microscopy13.10BO2-118[»]
4V6Telectron microscopy8.30AM2-115[»]
4V6Velectron microscopy9.80AM2-118[»]
4V6Yelectron microscopy12.00AM1-114[»]
4V6Zelectron microscopy12.00AM1-114[»]
4V70electron microscopy17.00AM1-114[»]
4V71electron microscopy20.00AM1-114[»]
4V72electron microscopy13.00AM1-114[»]
4V73electron microscopy15.00AM1-114[»]
4V74electron microscopy17.00AM1-114[»]
4V75electron microscopy12.00AM1-114[»]
4V76electron microscopy17.00AM1-114[»]
4V77electron microscopy17.00AM1-114[»]
4V78electron microscopy20.00AM1-114[»]
4V79electron microscopy15.00AM1-114[»]
4V7Aelectron microscopy9.00AM1-114[»]
4V7Belectron microscopy6.80AM1-118[»]
4V7Celectron microscopy7.60AM2-118[»]
4V7Delectron microscopy7.60BM2-118[»]
4V7Ielectron microscopy9.60BM1-118[»]
4V7SX-ray3.25AM2-115[»]
CM2-114[»]
4V7TX-ray3.19AM2-115[»]
CM2-114[»]
4V7UX-ray3.10AM/CM2-115[»]
4V7VX-ray3.29AM2-115[»]
CM2-114[»]
4V85X-ray3.20M1-118[»]
4V89X-ray3.70AM1-118[»]
4V9CX-ray3.30AM/CM1-118[»]
4V9DX-ray3.00AM/BM2-115[»]
4V9OX-ray2.90BM/DM/FM/HM1-118[»]
4V9PX-ray2.90BM/DM/FM/HM1-118[»]
4WF1X-ray3.09AM/CM2-115[»]
4WOIX-ray3.00AM/DM1-118[»]
4WWWX-ray3.10QM/XM2-115[»]
4YBBX-ray2.10AM/BM2-115[»]
5AFIelectron microscopy2.90m1-118[»]
5IQRelectron microscopy3.00r1-118[»]
5IT8X-ray3.12AM/BM2-115[»]
5J5BX-ray2.80AM/BM2-115[»]
5J7LX-ray3.00AM/BM2-115[»]
5J88X-ray3.32AM/BM2-115[»]
5J8AX-ray3.10AM/BM2-115[»]
5J91X-ray2.96AM/BM2-115[»]
5JC9X-ray3.03AM/BM2-115[»]
5JTEelectron microscopy3.60AM1-118[»]
5JU8electron microscopy3.60AM1-118[»]
5KCRelectron microscopy3.601m1-118[»]
5KCSelectron microscopy3.901m1-118[»]
5KPSelectron microscopy3.90181-118[»]
5KPVelectron microscopy4.10171-118[»]
5KPWelectron microscopy3.90171-118[»]
5KPXelectron microscopy3.90171-118[»]
5L3Pelectron microscopy3.70m1-118[»]
ProteinModelPortaliP0A7S9.
SMRiP0A7S9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-35855N.
IntActiP0A7S9. 101 interactors.
MINTiMINT-1290225.
STRINGi511145.b3298.

Chemistry databases

DrugBankiDB00560. Tigecycline.

Proteomic databases

EPDiP0A7S9.
PaxDbiP0A7S9.
PRIDEiP0A7S9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76323; AAC76323; b3298.
BAE77993; BAE77993; BAE77993.
GeneIDi947791.
KEGGiecj:JW3260.
eco:b3298.
PATRICi32122028. VBIEscCol129921_3391.

Organism-specific databases

EchoBASEiEB0905.
EcoGeneiEG10912. rpsM.

Phylogenomic databases

eggNOGiENOG4108Z04. Bacteria.
COG0099. LUCA.
HOGENOMiHOG000039879.
InParanoidiP0A7S9.
KOiK02952.
OMAiRTKNNSR.
PhylomeDBiP0A7S9.

Enzyme and pathway databases

BioCyciEcoCyc:EG10912-MONOMER.
ECOL316407:JW3260-MONOMER.
MetaCyc:EG10912-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A7S9.
PROiP0A7S9.

Family and domain databases

Gene3Di4.10.910.10. 1 hit.
HAMAPiMF_01315. Ribosomal_S13_S18. 1 hit.
InterProiIPR027437. 30s_Rbsml_prot_S13_C.
IPR001892. Ribosomal_S13.
IPR010979. Ribosomal_S13-like_H2TH.
IPR019980. Ribosomal_S13_bac-type.
IPR018269. Ribosomal_S13_CS.
[Graphical view]
PfamiPF00416. Ribosomal_S13. 1 hit.
[Graphical view]
PIRSFiPIRSF002134. Ribosomal_S13. 1 hit.
SUPFAMiSSF46946. SSF46946. 1 hit.
TIGRFAMsiTIGR03631. uS13_bact. 1 hit.
PROSITEiPS00646. RIBOSOMAL_S13_1. 1 hit.
PS50159. RIBOSOMAL_S13_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRS13_ECOLI
AccessioniPrimary (citable) accession number: P0A7S9
Secondary accession number(s): P02369, Q2M6W3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

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

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Ribosomal proteins
    Ribosomal proteins families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.