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P80373 (RS4_THET8) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
30S ribosomal protein S4
Gene names
Name:rpsD
Synonyms:rps4
Ordered Locus Names:TTHA1665
OrganismThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]
Taxonomic identifier300852 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length209 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation. HAMAP-Rule MF_01306_B

Cofactor

Binds 1 zinc ion per subunit Probable.

Subunit structure

Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.14 Ref.15

Sequence similarities

Belongs to the ribosomal protein S4P family.

Contains 1 S4 RNA-binding domain.

Mass spectrometry

Molecular mass is 24192 Da from positions 2 - 209. Determined by MALDI. Ref.4

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.3
Chain2 – 20920830S ribosomal protein S4 HAMAP-Rule MF_01306_B
PRO_0000132483

Regions

Domain99 – 16163S4 RNA-binding
Zinc finger9 – 3123C4-type HAMAP-Rule MF_01306_B

Sites

Metal binding91Zinc Probable
Metal binding121Zinc Probable
Metal binding261Zinc Probable
Metal binding311Zinc Probable

Experimental info

Sequence conflict121C → S AA sequence Ref.3
Sequence conflict261C → D AA sequence Ref.3

Secondary structure

.......................................... 209
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P80373 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 0FF3911816971236

FASTA20924,324
        10         20         30         40         50         60 
MGRYIGPVCR LCRREGVKLY LKGERCYSPK CAMERRPYPP GQHGQKRARR PSDYAVRLRE 

        70         80         90        100        110        120 
KQKLRRIYGI SERQFRNLFE EASKKKGVTG SVFLGLLESR LDNVVYRLGF AVSRRQARQL 

       130        140        150        160        170        180 
VRHGHITVNG RRVDLPSYRV RPGDEIAVAE KSRNLELIRQ NLEAMKGRKV GPWLSLDVEG 

       190        200 
MKGKFLRLPD REDLALPVNE QLVIEFYSR 

« Hide

References

« Hide 'large scale' references
[1]"Cloning of the RNA polymerase alpha subunit gene from Thermus thermophilus HB8 and characterization of the protein."
Wada T., Yamazaki T., Kuramitsu S., Kyogoku Y.
J. Biochem. 125:143-150(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete genome sequence of Thermus thermophilus HB8."
Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HB8 / ATCC 27634 / DSM 579.
[3]"Purification and characterization of the 30S ribosomal proteins from the bacterium Thermus thermophilus."
Tsiboli P., Herfurth E., Choli T.
Eur. J. Biochem. 226:169-177(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-27.
[4]"Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry."
Suh M.-J., Hamburg D.M., Gregory S.T., Dahlberg A.E., Limbach P.A.
Proteomics 5:4818-4831(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY.
[5]"Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution."
Clemons W.M. Jr., May J.L.C., Wimberly B.T., McCutcheon J.P., Capel M.S., Ramakrishnan V.
Nature 400:833-840(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE 30S SUBUNIT.
[6]"Structure of the 30S ribosomal subunit."
Wimberly B.T., Brodersen D.E., Clemons W.M. Jr., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., Ramakrishnan V.
Nature 407:327-339(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.05 ANGSTROMS) OF THE 30S SUBUNIT.
[7]"Structure of functionally activated small ribosomal subunit at 3.3 A resolution."
Schluenzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., Yonath A.
Cell 102:615-623(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 30S SUBUNIT.
[8]"The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit."
Brodersen D.E., Clemons W.M. Jr., Carter A.P., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V.
Cell 103:1143-1154(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 30S SUBUNIT.
[9]"Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics."
Carter A.P., Clemons W.M. Jr., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V.
Nature 407:340-348(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 30S SUBUNIT.
[10]"The path of messenger RNA through the ribosome."
Yusupova G.Z., Yusupov M.M., Cate J.H.D., Noller H.F.
Cell 106:233-241(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.0 ANGSTROMS) OF THE RIBOSOME.
[11]"Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3."
Pioletti M., Schluenzen F., Harms J., Zarivach R., Gluehmann M., Avila H., Bashan A., Bartels H., Auerbach T., Jacobi C., Hartsch T., Yonath A., Franceschi F.
EMBO J. 20:1829-1839(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF THE 30S SUBUNIT.
[12]"Crystal structure of an initiation factor bound to the 30S ribosomal subunit."
Carter A.P., Clemons W.M. Jr., Brodersen D.E., Morgan-Warren R.J., Hartsch T., Wimberly B.T., Ramakrishnan V.
Science 291:498-501(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF THE 30S SUBUNIT.
[13]"Crystal structure of the ribosome at 5.5 A resolution."
Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H.D., Noller H.F.
Science 292:883-896(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.
[14]"Recognition of cognate transfer RNA by the 30S ribosomal subunit."
Ogle J.M., Brodersen D.E., Clemons W.M. Jr., Tarry M.J., Carter A.P., Ramakrishnan V.
Science 292:897-902(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.11 ANGSTROMS) OF THE 30S SUBUNIT.
[15]"Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA."
Brodersen D.E., Clemons W.M. Jr., Carter A.P., Wimberly B.T., Ramakrishnan V.
J. Mol. Biol. 316:725-768(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.05 ANGSTROMS) OF THE 30S SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB024328 Genomic DNA. Translation: BAA75548.1.
AP008226 Genomic DNA. Translation: BAD71488.1.
RefSeqYP_144931.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1FJGX-ray3.00D1-209[»]
1FKAX-ray3.30D1-209[»]
1GIXX-ray5.50G1-209[»]
1HNWX-ray3.40D1-209[»]
1HNXX-ray3.40D1-209[»]
1HNZX-ray3.30D1-209[»]
1HR0X-ray3.20D1-209[»]
1I94X-ray3.20D2-209[»]
1I95X-ray4.50D2-209[»]
1I96X-ray4.20D2-209[»]
1I97X-ray4.50D2-209[»]
1IBKX-ray3.31D1-209[»]
1IBLX-ray3.11D1-209[»]
1IBMX-ray3.31D1-209[»]
1J5EX-ray3.05D2-209[»]
1JGOX-ray5.60F95-98[»]
G1-209[»]
1JGPX-ray7.00F95-98[»]
G1-209[»]
1JGQX-ray5.00F95-98[»]
G1-209[»]
1L1Umodel-D1-209[»]
1ML5electron microscopy14.00G1-209[»]
1N32X-ray3.00D2-209[»]
1N33X-ray3.35D2-209[»]
1N34X-ray3.80D2-209[»]
1N36X-ray3.65D2-209[»]
1PNSX-ray8.70D2-209[»]
1PNXX-ray9.50D2-209[»]
1QD7X-ray5.50C60-155[»]
1TWTmodel-G2-209[»]
1XMOX-ray3.25D1-209[»]
1XMQX-ray3.00D1-209[»]
1XNQX-ray3.05D1-209[»]
1XNRX-ray3.10D1-209[»]
1YL4X-ray5.50G1-209[»]
2B64X-ray5.90D1-209[»]
2B9MX-ray6.76D1-209[»]
2B9OX-ray6.46D1-209[»]
2E5LX-ray3.30D2-209[»]
2F4VX-ray3.80D1-209[»]
2HGIX-ray5.00G1-209[»]
2HGPX-ray5.50G1-209[»]
2HGRX-ray4.51G1-209[»]
2HHHX-ray3.35D1-209[»]
2J00X-ray2.80D2-208[»]
2J02X-ray2.80D2-208[»]
2OW8X-ray3.71e-[»]
2UU9X-ray3.10D2-208[»]
2UUAX-ray2.90D1-209[»]
2UUBX-ray2.90D2-208[»]
2UUCX-ray3.10D2-208[»]
2UXBX-ray3.10D1-209[»]
2UXCX-ray2.90D1-209[»]
2UXDX-ray3.20D1-209[»]
2V46X-ray3.80D2-208[»]
2V48X-ray3.50D1-209[»]
2VQEX-ray2.50D1-209[»]
2VQFX-ray2.90D1-209[»]
2WDGX-ray3.30D1-209[»]
2WDHX-ray3.30D1-209[»]
2WDKX-ray3.50D1-209[»]
2WDMX-ray3.50D1-209[»]
2WH1X-ray3.45D1-209[»]
2WH3X-ray3.45D1-209[»]
2WRIX-ray3.60D1-209[»]
2WRKX-ray3.60D1-209[»]
2WRNX-ray3.60D1-209[»]
2WRQX-ray3.60D1-209[»]
2X9RX-ray3.10D1-209[»]
2X9TX-ray3.10D1-209[»]
2XFZX-ray3.20D1-209[»]
2XG1X-ray3.20D1-209[»]
2XQDX-ray3.10D1-209[»]
2XSYelectron microscopy7.80D1-209[»]
2XUYelectron microscopy7.60D1-209[»]
2Y0UX-ray3.10D1-209[»]
2Y0WX-ray3.10D1-209[»]
2Y0YX-ray3.10D1-209[»]
2Y10X-ray3.10D1-209[»]
2Y12X-ray3.10D1-209[»]
2Y14X-ray3.10D1-209[»]
2Y16X-ray3.10D1-209[»]
2Y18X-ray3.10D1-209[»]
2ZKQelectron microscopy8.70d1-209[»]
2ZM6X-ray3.30D2-209[»]
3FICelectron microscopy6.40D2-209[»]
3HUWX-ray3.10D1-209[»]
3HUYX-ray3.10D1-209[»]
3I8GX-ray3.10G1-209[»]
3I8HX-ray3.10G1-209[»]
3I9BX-ray3.50G1-209[»]
3I9DX-ray3.50G1-209[»]
3KIQX-ray3.30d1-209[»]
3KISX-ray3.30d1-209[»]
3KIUX-ray3.60d1-209[»]
3KIXX-ray3.60d1-209[»]
3KNHX-ray3.00D1-209[»]
3KNJX-ray3.15D1-209[»]
3KNLX-ray3.45D1-209[»]
3KNNX-ray3.45D1-209[»]
3OGEX-ray3.00D1-209[»]
3OGYX-ray3.00D1-209[»]
3OHCX-ray3.00D1-209[»]
3OHDX-ray3.00D1-209[»]
3OHYX-ray3.00D1-209[»]
3OI0X-ray3.00D1-209[»]
3OI2X-ray3.10D1-209[»]
3OI4X-ray3.10D1-209[»]
3OTOX-ray3.69D1-209[»]
3T1HX-ray3.11D1-209[»]
3T1YX-ray2.80D1-209[»]
3TVFX-ray3.10G2-209[»]
3TVGX-ray3.10G2-209[»]
3UXSX-ray3.20D1-209[»]
3UXTX-ray3.20D1-209[»]
3UYDX-ray3.00G2-209[»]
3UYFX-ray3.00G2-209[»]
3UZ3X-ray3.30G2-209[»]
3UZ4X-ray3.30G2-209[»]
3UZ6X-ray3.00G2-209[»]
3UZ7X-ray3.00G2-209[»]
3UZGX-ray3.30G2-209[»]
3UZIX-ray3.30G2-209[»]
3UZLX-ray3.30G2-209[»]
3UZMX-ray3.30G2-209[»]
3V22X-ray3.00D1-209[»]
3V24X-ray3.00D1-209[»]
3V26X-ray3.10D1-209[»]
3V28X-ray3.10D1-209[»]
3V2CX-ray2.70D1-209[»]
3V2EX-ray2.70D1-209[»]
3V6UX-ray3.90D1-209[»]
3V6VX-ray3.90D1-209[»]
3ZN7X-ray3.10D1-209[»]
3ZNDX-ray3.10D1-209[»]
3ZVOX-ray3.80D1-209[»]
4ABRX-ray3.10D1-209[»]
4AQYX-ray3.50D2-209[»]
4B3MX-ray2.90D2-209[»]
4B3RX-ray3.00D2-209[»]
4B3SX-ray3.15D2-209[»]
4B3TX-ray3.00D2-209[»]
4B8FX-ray3.70D1-209[»]
4B8HX-ray3.70D1-209[»]
4BTCX-ray2.95D1-209[»]
4BYBX-ray3.35D1-209[»]
4BYDX-ray3.35D1-209[»]
4DH9X-ray3.20D1-209[»]
4DHBX-ray3.20D1-209[»]
4DR1X-ray3.60D1-209[»]
4DR2X-ray3.25D1-209[»]
4DR3X-ray3.35D1-209[»]
4DR4X-ray3.97D1-209[»]
4DR5X-ray3.45D1-209[»]
4DR6X-ray3.30D1-209[»]
4DR7X-ray3.75D1-209[»]
4DUYX-ray3.39D1-209[»]
4DUZX-ray3.65D1-209[»]
4DV0X-ray3.85D1-209[»]
4DV1X-ray3.85D1-209[»]
4DV2X-ray3.65D1-209[»]
4DV3X-ray3.55D1-209[»]
4DV4X-ray3.65D1-209[»]
4DV5X-ray3.68D1-209[»]
4DV6X-ray3.30D1-209[»]
4DV7X-ray3.29D1-209[»]
4EJ9X-ray3.52D1-209[»]
4EJAX-ray3.52D1-209[»]
4G5KX-ray3.30G2-209[»]
4G5MX-ray3.30G2-209[»]
4G5TX-ray3.10G2-209[»]
4G5VX-ray3.10G2-209[»]
4GKJX-ray3.30D2-209[»]
4GKKX-ray3.20D2-209[»]
4JI0X-ray3.49D1-209[»]
4JI1X-ray3.14D1-209[»]
4JI2X-ray3.64D1-209[»]
4JI3X-ray3.35D1-209[»]
4JI4X-ray3.69D1-209[»]
4JI5X-ray3.85D1-209[»]
4JI6X-ray3.55D1-209[»]
4JI7X-ray3.50D1-209[»]
4JI8X-ray3.74D1-209[»]
4JUWX-ray2.86D2-209[»]
4JV5X-ray3.16D2-209[»]
4JYAX-ray3.10D2-209[»]
4K0KX-ray3.40D2-209[»]
4K0LX-ray3.30D2-209[»]
4K0PX-ray3.30D2-209[»]
4KHPX-ray3.10D2-209[»]
ProteinModelPortalP80373.
SMRP80373. Positions 2-209.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING300852.TTHA1665.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD71488; BAD71488; BAD71488.
GeneID3168006.
KEGGttj:TTHA1665.
PATRIC23958285. VBITheThe93045_1635.

Phylogenomic databases

eggNOGCOG0522.
HOGENOMHOG000221004.
KOK02986.
OMATHGHILV.
OrthoDBEOG6N3CXM.
ProtClustDBPRK05327.

Enzyme and pathway databases

BioCycTTHE300852:GH8R-1704-MONOMER.

Family and domain databases

Gene3D1.10.1050.10. 1 hit.
3.10.290.10. 1 hit.
HAMAPMF_01306_B. Ribosomal_S4_B.
InterProIPR022801. Ribosomal_S4/S9.
IPR001912. Ribosomal_S4/S9_N.
IPR005709. Ribosomal_S4_bac-type.
IPR018079. Ribosomal_S4_CS.
IPR002942. S4_RNA-bd.
[Graphical view]
PANTHERPTHR11831. PTHR11831. 1 hit.
PfamPF00163. Ribosomal_S4. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]
SMARTSM00363. S4. 1 hit.
[Graphical view]
TIGRFAMsTIGR01017. rpsD_bact. 1 hit.
PROSITEPS00632. RIBOSOMAL_S4. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP80373.

Entry information

Entry nameRS4_THET8
AccessionPrimary (citable) accession number: P80373
Secondary accession number(s): Q5SHR5, Q9Z9H7
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: February 19, 2014
This is version 124 of the entry and version 3 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