Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000817
UniProt IDQ08211
Primary gene name(s)DHX9
Synonym gene name(s)DDX9, LKP, NDH2
Protein nameATP-dependent RNA helicase A
Protein functionUnwinds double-stranded DNA and RNA in a 3' to 5' direction. Alteration of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Component of the CRD-mediated complex that promotes MYC mRNA stability. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. As component of a large PER complex is involved in the inhibition of 3' transcriptional termination of circadian target genes such as PER1 and NR1D1 and the control of the circadian rhythms. Positively regulates HIV-1 LTR-directed gene expression. {ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:19229320, ECO:0000269|PubMed:22190748}.
Subcellular locationNucleus, nucleolus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Can shuttle between nucleus and cytoplasm.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q08211
Gene Ontology
(Biological Process)
Complete annatation
CRD-mediated mRNA stabilization [GO:0070934];
mRNA splicing, via spliceosome [GO:0000398];
osteoblast differentiation [GO:0001649];
positive regulation of type I interferon production [GO:0032481];
protein localization to cytoplasmic stress granule [GO:1903608];
rhythmic process [GO:0048511];
RNA processing [GO:0006396]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
ATP-dependent DNA helicase activity [GO:0004003];
ATP-dependent RNA helicase activity [GO:0004004];
DNA binding [GO:0003677];
poly(A RNA binding [GO:0044822];
RNA helicase activity [GO:0003724];
RNA polymerase II transcription factor binding [GO:0001085]
Gene Ontology
(Cellular Component)
Complete annatation
centrosome [GO:0005813];
CRD-mediated mRNA stability complex [GO:0070937];
cytoplasm [GO:0005737];
cytoplasmic ribonucleoprotein granule [GO:0036464];
cytosol [GO:0005829];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nuclear stress granule [GO:0097165];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction108025
Phylogenetic treeQ08211
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. CD31.18241881872030.0003563539770956580.00147351636290419
AZA vs. DISU0.3354481973178050.1857831867907130.772196340408505
AZA vs. IL70.312575109291710.1031120873563190.843852253376399
AZA vs. SAHA-0.1005120106049920.6795649298603480.906724266704883
DISU vs. CD3-0.8597400760111140.01882777069372030.0487989751730226
DISU vs. IL7-0.03166013877808890.9000049047891050.981521662424637
DISU vs. SAHA-0.434824414715690.1371416519966450.475413529527862
DMSO vs. AZA0.01203925234886450.9424654148764421
DMSO vs. CD3-1.182523614276270.0002560862183481620.00103596640156151
DMSO vs. DISU-0.325395162709060.183091710677860.697822984298268
DMSO vs. IL70.3078760553190910.08599054942367880.548585498333456
DMSO vs. SAHA-0.1193023589942020.6119656684671180.871830776400222
HIV vs. Mock in Activation0.0251969816283930.9677246506725190.999983755607037
HIV vs. Mock in Latency-0.04918254841428480.7650484810561790.999834320637052
IL7 vs. CD3-0.861714877320240.007625850774315320.0239268211326509
SAHA vs. CD3-1.307895936977030.000262518880872920.00111882339783792
SAHA vs. IL7-0.4167563677337940.08679001847160160.263711497367652
(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
-0.3484 0.02809

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) FALSE
(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 0.151896 0.350471
(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
1.035 1.04 1.016 0.97 1.003
(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
3LLM X-ray 2.8Å A/B=329-563.
3VYX X-ray 2.2Å A=152-264.
3VYY X-ray 2.9Å A/B=1-91.

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

HIV Partner Interaction Type PubMed
Gag-Pol complexes with 23125841
Pr55(Gag) interacts with 16527808
Nef complexes with 23125841
Tat interacts with 19454010
Pr55(Gag) enhanced by 20007598
Rev interacts with 22174317
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol regulated by 20007598
Nef regulated by 20007598
Vif regulated by 20007598
Rev regulated by 20007598
Pr55(Gag) complexes with 23125841
reverse transcriptase regulated by 20007598

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found