Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0006904
UniProt IDP62701
Primary gene name(s)RPS4X
Synonym gene name(s)CCG2, RPS4, SCAR
Protein name40S ribosomal protein S4, X isoform
Protein functionunknown
Subcellular locationCytoplasm {ECO:0000269|PubMed:17289661}. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P62701
Gene Ontology
(Biological Process)
Complete annatation
multicellular organism development [GO:0007275];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
positive regulation of cell proliferation [GO:0008284];
positive regulation of translation [GO:0045727];
response to ethanol [GO:0045471];
rRNA processing [GO:0006364];
SRP-dependent cotranslational protein targeting to membrane [GO:0006614];
translation [GO:0006412];
translational initiation [GO:0006413];
viral transcription [GO:0019083]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
rRNA binding [GO:0019843];
structural constituent of ribosome [GO:0003735]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasmic ribonucleoprotein granule [GO:0036464];
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];
nucleoplasm [GO:0005654];
polysome [GO:0005844];
ribosome [GO:0005840];
small ribosomal subunit [GO:0015935]
Protein-protein interaction112105
Phylogenetic treeP62701
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
Interferon-stimulated
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. CD3-0.1905246588285310.5601770629411220.670184846217541
AZA vs. DISU-0.04266582571530760.8656380276512680.991133096247651
AZA vs. IL70.005584269719894990.9767190512559540.999311006273513
AZA vs. SAHA-0.1720023100124660.4793622717378010.808696838080511
DISU vs. CD30.1347411134559210.7098795947247850.796540495078264
DISU vs. IL70.03928411519909450.8757388014766970.976126113490129
DISU vs. SAHA-0.1278656500913150.6599688332658490.895605472255214
DMSO vs. AZA0.01047055245959330.9498573420955011
DMSO vs. CD30.1862447577529020.5597943927919330.662266571965641
DMSO vs. DISU0.05032991841829320.8360668249471380.981844704166786
DMSO vs. IL70.002763802472739320.9876768811468860.998499429186965
DMSO vs. SAHA-0.1883779540252730.4228271785623850.761853855661689
HIV vs. Mock in Activation-0.2039081079966960.7429235987308750.999983755607037
HIV vs. Mock in Latency-0.2290182104093580.1632317635695380.999834320637052
IL7 vs. CD30.2042044392397180.5242235145856660.651357764021907
SAHA vs. CD3-0.006466385227767280.9853837743812280.990048235210688
SAHA vs. IL7-0.1812745332835160.4554154656633730.69265792850466
(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 -0.663702 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
0.972 0.973 0.932 0.907 0.863
(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
4UG0 EM - SE=1-263.
4V6X EM 5.0Å AE=1-263.
5A2Q EM 3.9Å E=1-263.

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

HIV Partner Interaction Type PubMed
Rev interacts with 22174317
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Pr55(Gag) complexes with 23125841
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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