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Protein

30S ribosomal protein S4

Gene

rpsD

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

Functioni

One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.1 Publication
With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).
Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.1 Publication
Protein S4 is also a translational repressor protein, it controls the translation of the alpha-operon (which codes for S13, S11, S4, RNA polymerase alpha subunit, and L17) by binding to its mRNA.1 Publication
Also functions as a rho-dependent antiterminator of rRNA transcription, increasing the synthesis of rRNA under conditions of excess protein, allowing a more rapid return to homeostasis. Binds directly to RNA polymerase.1 Publication

GO - Molecular functioni

  • mRNA 5'-UTR binding Source: EcoCyc
  • rRNA binding Source: EcoliWiki
  • structural constituent of ribosome Source: CAFA
  • translation repressor activity, mRNA regulatory element binding Source: EcoCyc

GO - Biological processi

Keywordsi

Molecular functionRepressor, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding
Biological processAntibiotic resistance, Transcription, Transcription regulation, Transcription termination, Translation regulation

Enzyme and pathway databases

BioCyciEcoCyc:EG10903-MONOMER
MetaCyc:EG10903-MONOMER

Protein family/group databases

MoonProtiP0A7V8

Names & Taxonomyi

Protein namesi
Recommended name:
30S ribosomal protein S4
Alternative name(s):
Small ribosomal subunit protein uS41 Publication
Gene namesi
Name:rpsD
Synonyms:ramA
Ordered Locus Names:b3296, JW3258
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10903 rpsD

Subcellular locationi

GO - Cellular componenti

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi44 – 47RKPR → AKPA: Decreases mRNA unwinding ability of the ribosome. 1 Publication4

Chemistry databases

DrugBankiDB00453 Clomocycline
DB00618 Demeclocycline
DB00254 Doxycycline
DB00256 Lymecycline
DB01017 Minocycline
DB00595 Oxytetracycline

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00001323802 – 20630S ribosomal protein S4Add BLAST205

Proteomic databases

EPDiP0A7V8
PaxDbiP0A7V8
PRIDEiP0A7V8

Interactioni

Subunit structurei

Part of the 30S ribosomal subunit (PubMed:4587210, PubMed:1100394, PubMed:7556101, PubMed:12809609, PubMed:16272117, PubMed:27934701, PubMed:10094780, PubMed:12244297, PubMed:27906160, PubMed:27906161, PubMed:28077875). Contacts protein S5. With proteins S3 and S5 encircles the mRNA as it enters the ribosome, which may play a role in mRNA helicase processivity (PubMed:15652481). Some nascent polypeptide chains are able to cross-link to this protein in situ (PubMed:9716382).13 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
rngP0A9J02EBI-543939,EBI-545964

Protein-protein interaction databases

BioGridi852105, 1 interactor
DIPiDIP-35794N
IntActiP0A7V8, 218 interactors
MINTiP0A7V8
STRINGi316385.ECDH10B_3471

Structurei

Secondary structure

1206
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0A7V8
SMRiP0A7V8
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7V8

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini96 – 156S4 RNA-bindingAdd BLAST61

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105G6W Bacteria
COG0522 LUCA
HOGENOMiHOG000221003
InParanoidiP0A7V8
KOiK02986
PhylomeDBiP0A7V8

Family and domain databases

CDDicd00165 S4, 1 hit
Gene3Di3.10.290.10, 1 hit
HAMAPiMF_01306_B Ribosomal_S4_B, 1 hit
InterProiView protein in InterPro
IPR022801 Ribosomal_S4/S9
IPR001912 Ribosomal_S4/S9_N
IPR005709 Ribosomal_S4_bac-type
IPR018079 Ribosomal_S4_CS
IPR002942 S4_RNA-bd
IPR036986 S4_RNA-bd_sf
PANTHERiPTHR11831 PTHR11831, 1 hit
PTHR11831:SF4 PTHR11831:SF4, 1 hit
PfamiView protein in Pfam
PF00163 Ribosomal_S4, 1 hit
PF01479 S4, 1 hit
SMARTiView protein in SMART
SM01390 Ribosomal_S4, 1 hit
SM00363 S4, 1 hit
TIGRFAMsiTIGR01017 rpsD_bact, 1 hit
PROSITEiView protein in PROSITE
PS00632 RIBOSOMAL_S4, 1 hit
PS50889 S4, 1 hit

Sequencei

Sequence statusi: Complete.

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

P0A7V8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD
60 70 80 90 100
YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGENL LALLEGRLDN
110 120 130 140 150
VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK
160 170 180 190 200
KQSRVKAALE LAEQREKPTW LEVDAGKMEG TFKRKPERSD LSADINEHLI

VELYSK
Length:206
Mass (Da):23,469
Last modified:January 23, 2007 - v2
Checksum:i4015969DF8E582BB
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti91Missing AA sequence (PubMed:4587210).Curated1
Sequence conflicti91Missing AA sequence (PubMed:1100394).Curated1
Sequence conflicti95E → Q AA sequence (PubMed:4587210).Curated1
Sequence conflicti95E → Q AA sequence (PubMed:1100394).Curated1
Sequence conflicti138 – 144SPNDVVS → DPNSVV AA sequence (PubMed:4587210).Curated7
Sequence conflicti138 – 144SPNDVVS → DPNSVV AA sequence (PubMed:1100394).Curated7
Sequence conflicti152Q → E AA sequence (PubMed:4587210).Curated1
Sequence conflicti152Q → E AA sequence (PubMed:1100394).Curated1
Sequence conflicti166E → Q AA sequence (PubMed:4587210).Curated1
Sequence conflicti166E → Q AA sequence (PubMed:1100394).Curated1

Mass spectrometryi

Molecular mass is 23339.5 Da from positions 2 - 206. Determined by MALDI. 1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti51Y → D in rpsD101; suppresses a temperature-sensitive mutant of release factor 1, R137P. Not a ram mutation. 1
Natural varianti170 – 206Missing in rpsD16; suppresses streptomycin dependence in protein S12. A ram mutation. Add BLAST37
Natural varianti177 – 206KMEGT…ELYSK → GRYV in rpsD12; suppresses streptomycin dependence in protein S12. A ram mutation. Add BLAST30
Natural varianti179 – 206EGTFK…ELYSK → ARYV in rpsD14; suppresses streptomycin dependence in protein S12. A ram mutation. Add BLAST28

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02543 Genomic DNA Translation: CAA26394.1
U18997 Genomic DNA Translation: AAA58094.1
U00096 Genomic DNA Translation: AAC76321.1
AP009048 Genomic DNA Translation: BAE77995.1
V00353 Genomic DNA Translation: CAA23645.1
J01685 Genomic DNA Translation: AAA24576.1
PIRiC23807 R3EC4
RefSeqiNP_417755.1, NC_000913.3
WP_000135224.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76321; AAC76321; b3296
BAE77995; BAE77995; BAE77995
GeneIDi35807177
947793
KEGGiecj:JW3258
eco:b3296
PATRICifig|1411691.4.peg.3435

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02543 Genomic DNA Translation: CAA26394.1
U18997 Genomic DNA Translation: AAA58094.1
U00096 Genomic DNA Translation: AAC76321.1
AP009048 Genomic DNA Translation: BAE77995.1
V00353 Genomic DNA Translation: CAA23645.1
J01685 Genomic DNA Translation: AAA24576.1
PIRiC23807 R3EC4
RefSeqiNP_417755.1, NC_000913.3
WP_000135224.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EG0electron microscopy11.50A43-200[»]
1M5Gmodel-D2-206[»]
2YKRelectron microscopy9.80D2-206[»]
3J9Yelectron microscopy3.90d1-206[»]
3J9Zelectron microscopy3.60SD2-206[»]
3JA1electron microscopy3.60SD2-206[»]
3JBUelectron microscopy3.64D1-206[»]
3JBVelectron microscopy3.32D1-206[»]
3JCDelectron microscopy3.70d1-206[»]
3JCEelectron microscopy3.20d1-206[»]
3JCJelectron microscopy3.70l1-206[»]
3JCNelectron microscopy4.60g1-206[»]
4A2Ielectron microscopy16.50D2-206[»]
4ADVelectron microscopy13.50D2-206[»]
4U1UX-ray2.95AD/CD2-206[»]
4U1VX-ray3.00AD/CD2-206[»]
4U20X-ray2.90AD/CD2-206[»]
4U24X-ray2.90AD/CD2-206[»]
4U25X-ray2.90AD/CD2-206[»]
4U26X-ray2.80AD/CD2-206[»]
4U27X-ray2.80AD/CD2-206[»]
4V47electron microscopy12.30BD2-206[»]
4V48electron microscopy11.50BD2-206[»]
4V4HX-ray3.46AD/CD1-206[»]
4V4QX-ray3.46AD/CD2-206[»]
4V4Velectron microscopy15.00AD3-206[»]
4V4Welectron microscopy15.00AD3-206[»]
4V50X-ray3.22AD/CD2-206[»]
4V52X-ray3.21AD/CD2-206[»]
4V53X-ray3.54AD/CD2-206[»]
4V54X-ray3.30AD/CD2-206[»]
4V55X-ray4.00AD/CD2-206[»]
4V56X-ray3.93AD/CD2-206[»]
4V57X-ray3.50AD/CD2-206[»]
4V5BX-ray3.74BD/DD2-206[»]
4V5Helectron microscopy5.80AD2-206[»]
4V5YX-ray4.45AD/CD2-206[»]
4V64X-ray3.50AD/CD2-206[»]
4V65electron microscopy9.00AR1-206[»]
4V66electron microscopy9.00AR1-206[»]
4V69electron microscopy6.70AD2-206[»]
4V6CX-ray3.19AD/CD1-206[»]
4V6DX-ray3.81AD/CD1-206[»]
4V6EX-ray3.71AD/CD1-206[»]
4V6Kelectron microscopy8.25BH1-206[»]
4V6Lelectron microscopy13.20AH1-206[»]
4V6Melectron microscopy7.10AD2-206[»]
4V6Nelectron microscopy12.10BG2-206[»]
4V6Oelectron microscopy14.70AG2-206[»]
4V6Pelectron microscopy13.50AG2-206[»]
4V6Qelectron microscopy11.50AG2-206[»]
4V6Relectron microscopy11.50AG2-206[»]
4V6Selectron microscopy13.10BF2-206[»]
4V6Telectron microscopy8.30AD2-206[»]
4V6Velectron microscopy9.80AD2-206[»]
4V6Yelectron microscopy12.00AD1-206[»]
4V6Zelectron microscopy12.00AD1-206[»]
4V70electron microscopy17.00AD1-206[»]
4V71electron microscopy20.00AD1-206[»]
4V72electron microscopy13.00AD1-206[»]
4V73electron microscopy15.00AD1-206[»]
4V74electron microscopy17.00AD1-206[»]
4V75electron microscopy12.00AD1-206[»]
4V76electron microscopy17.00AD1-206[»]
4V77electron microscopy17.00AD1-206[»]
4V78electron microscopy20.00AD1-206[»]
4V79electron microscopy15.00AD1-206[»]
4V7Aelectron microscopy9.00AD1-206[»]
4V7Belectron microscopy6.80AD1-206[»]
4V7Celectron microscopy7.60AD2-206[»]
4V7Delectron microscopy7.60BD2-206[»]
4V7Ielectron microscopy9.60BD1-206[»]
4V7SX-ray3.25AD/CD2-206[»]
4V7TX-ray3.19AD/CD2-206[»]
4V7UX-ray3.10AD/CD2-206[»]
4V7VX-ray3.29AD/CD2-206[»]
4V85X-ray3.20AD1-206[»]
4V89X-ray3.70AD1-206[»]
4V9CX-ray3.30AD/CD1-206[»]
4V9DX-ray3.00AD/BD2-206[»]
4V9OX-ray2.90BD/DD/FD/HD1-206[»]
4V9PX-ray2.90BD/DD/FD/HD1-206[»]
4WF1X-ray3.09AD/CD2-206[»]
4WOIX-ray3.00AD/DD1-206[»]
4WWWX-ray3.10QD/XD2-206[»]
4YBBX-ray2.10AD/BD2-206[»]
5AFIelectron microscopy2.90d1-206[»]
5H5Uelectron microscopy3.00k2-206[»]
5IQRelectron microscopy3.00i1-206[»]
5IT8X-ray3.12AD/BD2-206[»]
5J5BX-ray2.80AD/BD2-206[»]
5J7LX-ray3.00AD/BD2-206[»]
5J88X-ray3.32AD/BD2-206[»]
5J8AX-ray3.10AD/BD2-206[»]
5J91X-ray2.96AD/BD2-206[»]
5JC9X-ray3.03AD/BD2-206[»]
5JTEelectron microscopy3.60AD1-206[»]
5JU8electron microscopy3.60AD1-206[»]
5KCRelectron microscopy3.601d1-206[»]
5KCSelectron microscopy3.901d1-206[»]
5KPSelectron microscopy3.9091-206[»]
5KPVelectron microscopy4.1081-206[»]
5KPWelectron microscopy3.9081-206[»]
5KPXelectron microscopy3.9081-206[»]
5L3Pelectron microscopy3.70d1-206[»]
5LZAelectron microscopy3.60d2-206[»]
5LZBelectron microscopy5.30d2-206[»]
5LZCelectron microscopy4.80d2-206[»]
5LZDelectron microscopy3.40d2-206[»]
5LZEelectron microscopy3.50d2-206[»]
5LZFelectron microscopy4.60d2-206[»]
5MDVelectron microscopy2.97i1-206[»]
5MDWelectron microscopy3.06i1-206[»]
5MDYelectron microscopy3.35i1-206[»]
5MDZelectron microscopy3.10i1-206[»]
5ME0electron microscopy13.50D1-206[»]
5ME1electron microscopy13.50D1-206[»]
5MGPelectron microscopy3.10d2-206[»]
5MY1electron microscopy7.60D2-206[»]
5NO2electron microscopy5.16D2-206[»]
5NO3electron microscopy5.16D2-206[»]
5NO4electron microscopy5.16D2-206[»]
5NP6electron microscopy3.60G2-206[»]
5NWYelectron microscopy2.9331-206[»]
5O2Relectron microscopy3.40d2-206[»]
5U4Ielectron microscopy3.50d1-206[»]
5U4Jelectron microscopy3.70d1-206[»]
5U9Felectron microscopy3.20D1-206[»]
5U9Gelectron microscopy3.20D1-206[»]
5UYKelectron microscopy3.90D2-206[»]
5UYLelectron microscopy3.60D2-206[»]
5UYMelectron microscopy3.20D2-206[»]
5UYNelectron microscopy4.00D2-206[»]
5UYPelectron microscopy3.90D2-206[»]
5UYQelectron microscopy3.80D2-206[»]
5UZ4electron microscopy5.80D1-206[»]
5WDTelectron microscopy3.00d2-206[»]
5WE4electron microscopy3.10d2-206[»]
5WE6electron microscopy3.40d2-206[»]
5WFKelectron microscopy3.40d2-206[»]
6BU8electron microscopy3.50D2-206[»]
6C4Ielectron microscopy3.24d1-206[»]
6ENFelectron microscopy3.20d2-206[»]
6ENJelectron microscopy3.70d2-206[»]
6ENUelectron microscopy3.10d2-206[»]
6GWTelectron microscopy3.80d2-206[»]
6GXMelectron microscopy3.80d2-206[»]
6GXNelectron microscopy3.90d2-206[»]
6GXOelectron microscopy3.90d2-206[»]
6GXPelectron microscopy4.40d2-206[»]
6H4Nelectron microscopy3.00d2-206[»]
6H58electron microscopy7.90d/dd2-206[»]
ProteinModelPortaliP0A7V8
SMRiP0A7V8
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi852105, 1 interactor
DIPiDIP-35794N
IntActiP0A7V8, 218 interactors
MINTiP0A7V8
STRINGi316385.ECDH10B_3471

Chemistry databases

DrugBankiDB00453 Clomocycline
DB00618 Demeclocycline
DB00254 Doxycycline
DB00256 Lymecycline
DB01017 Minocycline
DB00595 Oxytetracycline

Protein family/group databases

MoonProtiP0A7V8

Proteomic databases

EPDiP0A7V8
PaxDbiP0A7V8
PRIDEiP0A7V8

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76321; AAC76321; b3296
BAE77995; BAE77995; BAE77995
GeneIDi35807177
947793
KEGGiecj:JW3258
eco:b3296
PATRICifig|1411691.4.peg.3435

Organism-specific databases

EchoBASEiEB0896
EcoGeneiEG10903 rpsD

Phylogenomic databases

eggNOGiENOG4105G6W Bacteria
COG0522 LUCA
HOGENOMiHOG000221003
InParanoidiP0A7V8
KOiK02986
PhylomeDBiP0A7V8

Enzyme and pathway databases

BioCyciEcoCyc:EG10903-MONOMER
MetaCyc:EG10903-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0A7V8
PROiPR:P0A7V8

Family and domain databases

CDDicd00165 S4, 1 hit
Gene3Di3.10.290.10, 1 hit
HAMAPiMF_01306_B Ribosomal_S4_B, 1 hit
InterProiView protein in InterPro
IPR022801 Ribosomal_S4/S9
IPR001912 Ribosomal_S4/S9_N
IPR005709 Ribosomal_S4_bac-type
IPR018079 Ribosomal_S4_CS
IPR002942 S4_RNA-bd
IPR036986 S4_RNA-bd_sf
PANTHERiPTHR11831 PTHR11831, 1 hit
PTHR11831:SF4 PTHR11831:SF4, 1 hit
PfamiView protein in Pfam
PF00163 Ribosomal_S4, 1 hit
PF01479 S4, 1 hit
SMARTiView protein in SMART
SM01390 Ribosomal_S4, 1 hit
SM00363 S4, 1 hit
TIGRFAMsiTIGR01017 rpsD_bact, 1 hit
PROSITEiView protein in PROSITE
PS00632 RIBOSOMAL_S4, 1 hit
PS50889 S4, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRS4_ECOLI
AccessioniPrimary (citable) accession number: P0A7V8
Secondary accession number(s): P02354, Q2M6W1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 7, 2018
This is version 147 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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