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P0A7S9 (RS13_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
30S ribosomal protein S13
Gene names
Name:rpsM
Ordered Locus Names:b3298, JW3260
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length118 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. Ref.11

In the E.coli 70S ribosome in the initiation state (Ref.14) 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 (Ref.14). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (Ref.15), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (Ref.16) 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. Ref.11

Contacts the tRNAs in the A and P sites. Ref.11

The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Ref.11

Subunit structure

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. Ref.14 Ref.15

Sequence similarities

Belongs to the ribosomal protein S13P family.

Mass spectrometry

Molecular mass is 12968.1 Da from positions 2 - 118. Determined by MALDI. Ref.12

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4
Chain2 – 11811730S ribosomal protein S13 HAMAP-Rule MF_01315
PRO_0000132089

Natural variations

Natural variant89 – 9911Missing in PW118; partially suppresses a rimM deletion.
Natural variant100 – 11819Missing in rpsM413; pseudorevertant of streptomycin resistance. A strong antisuppressor of two tRNA suppressors, decreases translation step time and growth rate.
Natural variant1051N → H in PW095; partially suppresses a rimM deletion.
Natural variant1051N → K in PW097; partially suppresses a rimM deletion.

Experimental info

Mutagenesis83 – 11836Missing: Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro.
Mutagenesis114 – 1185Missing: Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro.

Secondary structure

............................. 118
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A7S9 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 6277C365EBE4F732

FASTA11813,099
        10         20         30         40         50         60 
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV 

        70         80         90        100        110 
AKFVVEGDLR REISMSIKRL MDLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKPIKK 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli."
Bedwell D.M., Davis G.R., Gosink M., Post L.E., Nomura M., Kestler H., Zengel J.M., Lindahl L.
Nucleic Acids Res. 13:3891-3903(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Primary structure of protein S13 from the small subunit of Escherichia coli ribosomes."
Lindemann H., Wittmann-Liebold B.
Hoppe-Seyler's Z. Physiol. Chem. 358:843-863(1977) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-118.
Strain: K.
[5]"DNA sequence of the promoter region for the alpha ribosomal protein operon in Escherichia coli."
Post L.E., Arfsten A.E., Davis G.R., Nomura M.
J. Biol. Chem. 255:4653-4659(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-36.
[6]"Growth-rate-dependent regulation of ribosome synthesis in E. coli: expression of the lacZ and galK genes fused to ribosomal promoters."
Miura A., Krueger J.H., Itoh S., de Boer H.A., Nomura M.
Cell 25:773-782(1981) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-36.
[7]"Identification of a cross-link in the Escherichia coli ribosomal protein pair S13-S19 at the amino acid level."
Pohl T., Wittmann-Liebold B.
J. Biol. Chem. 263:4293-4301(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 83-85, CROSS-LINKING TO S19.
Strain: K12 / A19.
[8]"Antisuppression by a mutation in rpsM(S13) giving a shortened ribosomal protein S13."
Faxen M., Walles-Granberg A., Isaksson L.A.
Biochim. Biophys. Acta 1218:27-34(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF VARIANT RPSM413.
Strain: K12.
[9]"The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site."
Osswald M., Doering T., Brimacombe R.
Nucleic Acids Res. 23:4635-4641(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: CROSS-LINKING TO THE TRNA CENTRAL FOLD.
Strain: MRE-600.
[10]"A novel ribosome-associated protein is important for efficient translation in Escherichia coli."
Bylund G.O., Persson B.C., Lundberg L.A., Wikstroem P.M.
J. Bacteriol. 179:4567-4574(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: ABILITY OF VARIANTS PW118; PW097 AND PW095 TO PARTIALLY SUPPRESS A RIMM DELETION.
Strain: MW100.
[11]"Creating ribosomes with an all-RNA 30S subunit P site."
Hoang L., Fredrick K., Noller H.F.
Proc. Natl. Acad. Sci. U.S.A. 101:12439-12443(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: ROLE IN P SITE TRNA-BINDING, MUTAGENESIS.
Strain: CSH142.
[12]"Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry."
Arnold R.J., Reilly J.P.
Anal. Biochem. 269:105-112(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY.
Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[13]"All-atom homology model of the Escherichia coli 30S ribosomal subunit."
Tung C.-S., Joseph S., Sanbonmatsu K.Y.
Nat. Struct. Biol. 9:750-755(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING.
[14]"Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement."
Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J.
Cell 113:789-801(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (11.50 ANGSTROMS), INTERSUBUNIT BRIDGE FORMATION.
Strain: MRE-600.
[15]"Structures of the bacterial ribosome at 3.5 A resolution."
Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., Cate J.H.D.
Science 310:827-834(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.46 ANGSTROMS) OF 2 DIFFERENT RIBOSOME STRUCTURES INCLUDING THE INTERSUBUNIT BRIDGE B1B.
Strain: MRE-600.
[16]"Locking and unlocking of ribosomal motions."
Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., Frank J.
Cell 114:123-134(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING OF RIBOSOMAL COMPLEXES INCLUDING BRIDGE CHANGES UPON TRANSLOCATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRR3EC13. A23807.
RefSeqNP_417757.1. NC_000913.3.
YP_492134.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1M5Gmodel-M2-118[»]
1P6Gelectron microscopy12.30M2-118[»]
1P87electron microscopy11.50M2-118[»]
1VS5X-ray3.46M1-118[»]
1VS7X-ray3.46M1-118[»]
2AVYX-ray3.46M2-118[»]
2AW7X-ray3.46M2-118[»]
2GY9electron microscopy15.00M2-115[»]
2GYBelectron microscopy15.00M2-115[»]
2I2PX-ray3.22M2-117[»]
2I2UX-ray3.22M2-117[»]
2QALX-ray3.21M2-118[»]
2QANX-ray3.21M2-118[»]
2QB9X-ray3.54M2-118[»]
2QBBX-ray3.54M2-118[»]
2QBDX-ray3.30M2-118[»]
2QBFX-ray3.30M2-118[»]
2QBHX-ray4.00M2-118[»]
2QBJX-ray4.00M2-118[»]
2QOUX-ray3.93M2-118[»]
2QOWX-ray3.93M2-118[»]
2QOYX-ray3.50M2-118[»]
2QP0X-ray3.50M2-118[»]
2VHOX-ray3.74M2-118[»]
2VHPX-ray3.74M2-118[»]
2WWLelectron microscopy5.80M2-114[»]
2YKRelectron microscopy9.80M2-115[»]
2Z4KX-ray4.45M2-118[»]
2Z4MX-ray4.45M2-118[»]
3DF1X-ray3.50M2-117[»]
3DF3X-ray3.50M2-117[»]
3E1Aelectron microscopy-F1-118[»]
3E1Celectron microscopy-F1-118[»]
3FIHelectron microscopy6.70M2-114[»]
3I1MX-ray3.19M1-118[»]
3I1OX-ray3.19M1-118[»]
3I1QX-ray3.81M1-118[»]
3I1SX-ray3.81M1-118[»]
3I1ZX-ray3.71M1-118[»]
3I21X-ray3.71M1-118[»]
3IZVelectron microscopy-Q1-118[»]
3IZWelectron microscopy-Q1-118[»]
3J00electron microscopy-M2-118[»]
3J0Uelectron microscopy12.10P2-118[»]
3J0Velectron microscopy14.70P2-118[»]
3J0Xelectron microscopy13.50P2-118[»]
3J0Zelectron microscopy11.50P2-118[»]
3J10electron microscopy11.50P2-118[»]
3J13electron microscopy13.10O2-118[»]
3J18electron microscopy8.30M2-115[»]
3J36electron microscopy9.80M2-118[»]
3J4Velectron microscopy12.00M1-114[»]
3J4Welectron microscopy12.00M1-114[»]
3J4Yelectron microscopy17.00M1-114[»]
3J4Zelectron microscopy20.00M1-114[»]
3J53electron microscopy13.00M1-114[»]
3J55electron microscopy15.00M1-114[»]
3J57electron microscopy17.00M1-114[»]
3J59electron microscopy12.00M1-114[»]
3J5Belectron microscopy17.00M1-114[»]
3J5Delectron microscopy17.00M1-114[»]
3J5Felectron microscopy20.00M1-114[»]
3J5Helectron microscopy15.00M1-114[»]
3J5Jelectron microscopy9.00M1-114[»]
3J5Nelectron microscopy6.80M1-118[»]
3J5Telectron microscopy7.60M2-118[»]
3J5Xelectron microscopy7.60M2-118[»]
3KC4electron microscopy-M1-118[»]
3OAQX-ray3.25M2-115[»]
3OARX-ray3.25M2-114[»]
3OFAX-ray3.19M2-115[»]
3OFBX-ray3.19M2-114[»]
3OFOX-ray3.10M2-115[»]
3OFPX-ray3.10M2-114[»]
3OFXX-ray3.29M2-115[»]
3OFYX-ray3.29M2-114[»]
3OR9X-ray3.30M1-118[»]
3ORAX-ray3.30M1-118[»]
3SFSX-ray3.20M1-118[»]
3UOQX-ray3.70M1-118[»]
4A2Ielectron microscopy16.50M2-115[»]
4ADVelectron microscopy13.50M2-118[»]
4GAQX-ray3.30M1-118[»]
4GASX-ray3.30M1-118[»]
4GD1X-ray3.00M2-115[»]
4GD2X-ray3.00M2-115[»]
4KIYX-ray2.90M1-118[»]
4KJ0X-ray2.90M1-118[»]
4KJ2X-ray2.90M1-118[»]
4KJ4X-ray2.90M1-118[»]
4KJ6X-ray2.90M1-118[»]
4KJ8X-ray2.90M1-118[»]
4KJAX-ray2.90M1-118[»]
4KJCX-ray2.90M1-118[»]
ProteinModelPortalP0A7S9.
SMRP0A7S9. Positions 2-116.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-35855N.
IntActP0A7S9. 101 interactions.
MINTMINT-1290225.
STRING511145.b3298.

Chemistry

ChEMBLCHEMBL2363135.

Proteomic databases

PaxDbP0A7S9.
PRIDEP0A7S9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76323; AAC76323; b3298.
BAE77993; BAE77993; BAE77993.
GeneID12934445.
947791.
KEGGecj:Y75_p3878.
eco:b3298.
PATRIC32122028. VBIEscCol129921_3391.

Organism-specific databases

EchoBASEEB0905.
EcoGeneEG10912. rpsM.

Phylogenomic databases

eggNOGCOG0099.
HOGENOMHOG000039879.
KOK02952.
OMAREVAMNI.
OrthoDBEOG618R01.
PhylomeDBP0A7S9.
ProtClustDBPRK05179.

Enzyme and pathway databases

BioCycEcoCyc:EG10912-MONOMER.
ECOL316407:JW3260-MONOMER.

Gene expression databases

GenevestigatorP0A7S9.

Family and domain databases

Gene3D4.10.910.10. 1 hit.
HAMAPMF_01315. Ribosomal_S13_S18.
InterProIPR027437. 30s_Rbsml_prot_S13_C.
IPR001892. Ribosomal_S13.
IPR010979. Ribosomal_S13-like_H2TH.
IPR019980. Ribosomal_S13_bac-type.
IPR018269. Ribosomal_S13_CS.
[Graphical view]
PfamPF00416. Ribosomal_S13. 1 hit.
[Graphical view]
PIRSFPIRSF002134. Ribosomal_S13. 1 hit.
SUPFAMSSF46946. SSF46946. 1 hit.
TIGRFAMsTIGR03631. bact_S13. 1 hit.
PROSITEPS00646. RIBOSOMAL_S13_1. 1 hit.
PS50159. RIBOSOMAL_S13_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0A7S9.
PROP0A7S9.

Entry information

Entry nameRS13_ECOLI
AccessionPrimary (citable) accession number: P0A7S9
Secondary accession number(s): P02369, Q2M6W3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene