Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0006902
UniProt IDP23396
Primary gene name(s)RPS3
Synonym gene name(s)unknown
Protein name40S ribosomal protein S3
Protein functionInvolved in translation as a component of the 40S small ribosomal subunit, PubMed:8706699. Has endonuclease activity and plays a role in repair of damaged DNA, PubMed:7775413. Cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA, PubMed:15707971. Displays high binding affinity for 7,8-dihydro-8-oxoguanine, 8-oxoG, a common DNA lesion caused by reactive oxygen species, ROS, PubMed:14706345. Has also been shown to bind with similar affinity to intact and damaged DNA, PubMed:18610840. Stimulates the N-glycosylase activity of the base excision protein OGG1, PubMed:15518571. Enhances the uracil excision activity of UNG1, PubMed:18973764. Also stimulates the cleavage of the phosphodiester backbone by APEX1, PubMed:18973764. When located in the mitochondrion, reduces cellular ROS levels and mitochondrial DNA damage, PubMed:23911537. Has also been shown to negatively regulate DNA repair in cells exposed to hydrogen peroxide, PubMed:17049931. Plays a role in regulating transcription as part of the NF-kappa-B p65-p50 complex where it binds to the RELA/p65 subunit, enhances binding of the complex to DNA and promotes transcription of target genes, PubMed:18045535. Represses its own translation by binding to its cognate mRNA, PubMed:20217897. Binds to and protects TP53/p53 from MDM2-mediated ubiquitination, PubMed:19656744. Involved in spindle formation and chromosome movement during mitosis by regulating microtubule polymerization, PubMed:23131551. Involved in induction of apoptosis through its role in activation of CASP8, PubMed:14988002. Induces neuronal apoptosis by interacting with the E2F1 transcription factor and acting synergistically with it to up-regulate pro-apoptotic proteins BCL2L11/BIM and HRK/Dp5, PubMed:20605787. Interacts with TRADD following exposure to UV radiation and induces apoptosis by caspase-dependent JNK activation, PubMed:22510408. {ECO:0000269|PubMed:14706345, ECO:0000269|PubMed:14988002, ECO:0000269|PubMed:15518571, ECO:0000269|PubMed:15707971, ECO:0000269|PubMed:17049931, ECO:0000269|PubMed:18045535, ECO:0000269|PubMed:18610840, ECO:0000269|PubMed:18973764, ECO:0000269|PubMed:19656744, ECO:0000269|PubMed:20217897, ECO:0000269|PubMed:20605787, ECO:0000269|PubMed:22510408, ECO:0000269|PubMed:23131551, ECO:0000269|PubMed:23911537, ECO:0000269|PubMed:7775413, ECO:0000269|PubMed:8706699}.
Subcellular locationCytoplasm {ECO:0000269|PubMed:16314389, ECO:0000269|PubMed:17289661, ECO:0000269|PubMed:17560175, ECO:0000269|PubMed:18045535, ECO:0000269|PubMed:20217897, ECO:0000269|PubMed:21871177}. Nucleus {ECO:0000269|PubMed:17560175, ECO:0000269|PubMed:18045535, ECO:0000269|PubMed:19460357, ECO:0000269|PubMed:20217897, ECO:0000269|PubMed:21871177}. Nucleus, nucleolus {ECO:0000269|PubMed:16314389, ECO:0000269|PubMed:19460357}. Mitochondrion inner membrane {ECO:0000269|PubMed:23911537};
Peripheral membrane protein {ECO:0000269|PubMed:23911537}. Cytoplasm, cytoskeleton, spindle {ECO:0000269|PubMed:23131551}. Note=In normal cells, located mainly in the cytoplasm with small amounts in the nucleus but translocates to the nucleus in cells undergoing apoptosis, By similarity. Nuclear translocation is induced by DNA damaging agents such as hydrogen peroxide, PubMed:17560175. Accumulates in the mitochondrion in response to increased ROS levels, PubMed:23911537. Localizes to the spindle during mitosis, PubMed:23131551. Localized in cytoplasmic mRNP granules containing untranslated mRNAs, PubMed:17289661. {ECO:0000250|UniProtKB:P62908, ECO:0000269|PubMed:17289661, ECO:0000269|PubMed:17560175, ECO:0000269|PubMed:23131551, ECO:0000269|PubMed:23911537}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P23396
Gene Ontology
(Biological Process)
Complete annatation
apoptotic process [GO:0006915];
cell division [GO:0051301];
cellular response to DNA damage stimulus [GO:0006974];
cellular response to hydrogen peroxide [GO:0070301];
chromosome segregation [GO:0007059];
DNA damage response, detection of DNA damage [GO:0042769];
DNA repair [GO:0006281];
mitotic nuclear division [GO:0007067];
negative regulation of DNA repair [GO:0045738];
negative regulation of protein ubiquitination [GO:0031397];
negative regulation of translation [GO:0017148];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
positive regulation of apoptotic signaling pathway [GO:2001235];
positive regulation of base-excision repair [GO:1905053];
positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis [GO:2001272];
positive regulation of DNA N-glycosylase activity [GO:1902546];
positive regulation of DNA repair [GO:0045739];
positive regulation of endodeoxyribonuclease activity [GO:0032079];
positive regulation of gene expression [GO:0010628];
positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage [GO:1902231];
positive regulation of JUN kinase activity [GO:0043507];
positive regulation of microtubule polymerization [GO:0031116];
positive regulation of NIK/NF-kappaB signaling [GO:1901224];
regulation of apoptotic process [GO:0042981];
regulation of transcription, DNA-templated [GO:0006355];
response to oxidative stress [GO:0006979];
response to TNF agonist [GO:0061481];
rRNA processing [GO:0006364];
spindle assembly [GO:0051225];
SRP-dependent cotranslational protein targeting to membrane [GO:0006614];
transcription, DNA-templated [GO:0006351];
translation [GO:0006412];
translational initiation [GO:0006413];
viral transcription [GO:0019083]
Gene Ontology
(Molecular Function)
Complete annatation
damaged DNA binding [GO:0003684];
DNA-(apurinic or apyrimidinic site lyase activity [GO:0003906];
DNA binding [GO:0003677];
endodeoxyribonuclease activity [GO:0004520];
enzyme binding [GO:0019899];
Hsp70 protein binding [GO:0030544];
Hsp90 protein binding [GO:0051879];
iron-sulfur cluster binding [GO:0051536];
kinase binding [GO:0019900];
microtubule binding [GO:0008017];
mRNA binding [GO:0003729];
NF-kappaB binding [GO:0051059];
oxidized purine DNA binding [GO:0032357];
oxidized purine nucleobase lesion DNA N-glycosylase activity [GO:0008534];
oxidized pyrimidine DNA binding [GO:0032358];
poly(A RNA binding [GO:0044822];
protein kinase A binding [GO:0051018];
protein kinase binding [GO:0019901];
RNA binding [GO:0003723];
small ribosomal subunit rRNA binding [GO:0070181];
structural constituent of ribosome [GO:0003735];
SUMO binding [GO:0032183];
supercoiled DNA binding [GO:0097100];
transcription factor binding [GO:0008134];
tubulin binding [GO:0015631];
ubiquitin-like protein conjugating enzyme binding [GO:0044390]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytosol [GO:0005829];
cytosolic small ribosomal subunit [GO:0022627];
extracellular exosome [GO:0070062];
focal adhesion [GO:0005925];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
mitochondrial inner membrane [GO:0005743];
mitochondrial matrix [GO:0005759];
mitotic spindle [GO:0072686];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
plasma membrane [GO:0005886];
polysome [GO:0005844];
ribosome [GO:0005840];
ruffle membrane [GO:0032587]
Protein-protein interaction112102
Phylogenetic treeP23396
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD3-0.6277751344173110.05555093586153630.109089733590238
AZA vs. DISU-0.07789680098623380.7573711785784090.976021571236163
AZA vs. IL7-0.05302109857668440.7817336994014970.999311006273513
AZA vs. SAHA-0.1372943328878950.5723192862406570.857824492472075
DISU vs. CD30.5375524751830940.1382416316318680.24043548577579
DISU vs. IL70.01532846787827550.9513362714447670.991359346324962
DISU vs. SAHA-0.0574492343776760.8433023759066120.958718383732077
DMSO vs. AZA-0.04187205671065020.8014795768344141
DMSO vs. CD30.5743258419910930.0727915710128130.131629458325294
DMSO vs. DISU0.03405289680626730.8886651481910290.987802141379617
DMSO vs. IL7-0.003922459672301780.9825095599050610.997933675755882
DMSO vs. SAHA-0.1016964966541950.6651372994956840.894993655464127
HIV vs. Mock in Activation0.002817078407765770.9963985552386440.999983755607037
HIV vs. Mock in Latency-0.202592855968510.217364120758120.999834320637052
IL7 vs. CD30.5815647202535720.07059095531789680.144391025852444
SAHA vs. CD30.4663303428977960.1868000730718760.286230513593612
SAHA vs. IL7-0.08717557983662440.7194688153072620.870845788104021
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) unknown
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK -0.928823 0.000305467
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.03 0.974 0.911 0.861 0.916
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1WH9 NMR - A=17-95.
4UG0 EM - SD=1-243.
4V6X EM 5.0Å AD=1-243.
5A2Q EM 3.9Å D=1-243.
5AJ0 EM 3.5Å BD=1-243.
5FLX EM 3.9Å D=1-243.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Pr55(Gag) complexes with 23125841
Pr55(Gag) interacts with 26362536
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03010 Ribosome - Homo sapiens (human)