Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000773
UniProt IDQ92499
Primary gene name(s)DDX1
Synonym gene name(s)unknown
Protein nameATP-dependent RNA helicase DDX1
Protein functionActs as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks, DSBs, thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF-kappa-B promoter region via association with RELA. Binds to poly(A RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease, ZBTB8OS, acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation, PubMed:24870230. Required for HIV-1 Rev function as well as for HIV-1 replication. Binds to the RRE sequence of HIV-1 mRNAs. {ECO:0000269|PubMed:12183465, ECO:0000269|PubMed:15567440, ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:18710941, ECO:0000269|PubMed:20573827, ECO:0000269|PubMed:24870230}.
Subcellular locationNucleus. Cytoplasm. Cytoplasmic granule. Note=Localized with MBNL1, TIAL1 and YBX1 in stress granules upon stress. Localized with CSTF2 in cleavage bodies. Forms large aggregates called DDX1 bodies. Relocalized into multiple foci, IR-induced foci or IRIF after IR treatment, a process that depends on the presence of chromosomal DNA and/or RNA-DNA duplexes. Relocalized at sites of DNA double-strand breaks, DSBs in an ATM-dependent manner after IR treatment. Colocalized with RELA in the nucleus upon TNF-alpha induction. Relocalized to the cytoplasm with a perinuclear staining pattern in avian infectious bronchitis virus, IBV-infected cells. Required for proper localization of HIV-1 Rev. Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low, PubMed:24608264. {ECO:0000269|PubMed:24608264}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92499
Gene Ontology
(Biological Process)
Complete annatation
DNA duplex unwinding [GO:0032508];
double-strand break repair [GO:0006302];
multicellular organism development [GO:0007275];
protein localization to cytoplasmic stress granule [GO:1903608];
regulation of transcription, DNA-templated [GO:0006355];
regulation of translational initiation [GO:0006446];
response to exogenous dsRNA [GO:0043330];
response to virus [GO:0009615];
RNA secondary structure unwinding [GO:0010501];
spliceosomal complex assembly [GO:0000245];
transcription, DNA-templated [GO:0006351];
tRNA splicing, via endonucleolytic cleavage and ligation [GO:0006388]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
ATP-dependent helicase activity [GO:0008026];
ATP-dependent RNA helicase activity [GO:0004004];
chromatin binding [GO:0003682];
DNA/RNA helicase activity [GO:0033677];
DNA binding [GO:0003677];
double-stranded RNA binding [GO:0003725];
exonuclease activity [GO:0004527];
nuclease activity [GO:0004518];
poly(A binding [GO:0008143];
poly(A RNA binding [GO:0044822];
RNA helicase activity [GO:0003724];
transcription cofactor activity [GO:0003712]
Gene Ontology
(Cellular Component)
Complete annatation
cleavage body [GO:0071920];
cytoplasm [GO:0005737];
cytoplasmic stress granule [GO:0010494];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
tRNA-splicing ligase complex [GO:0072669]
Protein-protein interaction108019
Phylogenetic treeQ92499
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. CD31.644528873750679.63454603541969e-077.49674124139626e-06
AZA vs. DISU0.08173459815675050.7464739933204340.976008954784031
AZA vs. IL70.3152279856471530.1013614820325270.84139376197593
AZA vs. SAHA-0.2636994346785080.2801580274767480.653092699754103
DISU vs. CD3-1.575593144448342.13605022925112e-050.000145170519187247
DISU vs. IL70.2246736922106440.3723086151909050.74539980837679
DISU vs. SAHA-0.3444646966277050.2374631552046940.616020608743524
DMSO vs. AZA-0.01801391250966910.9144528675603331
DMSO vs. CD3-1.674418345878863.42376037298919e-072.67664504510027e-06
DMSO vs. DISU-0.1017300209010480.6766469038279750.955350023416557
DMSO vs. IL70.3405095679980130.05850379204502040.468821519029444
DMSO vs. SAHA-0.2526531184108170.2845119552112990.634959229526061
HIV vs. Mock in Activation-0.1726224769290980.7812626993103160.999983755607037
HIV vs. Mock in Latency0.0224751692912590.891820154248990.999834320637052
IL7 vs. CD3-1.320728071266515.24067536714634e-050.000331067476148352
SAHA vs. CD3-1.933137203428221.20305633788398e-071.23670252468701e-06
SAHA vs. IL7-0.58247759820290.01711892347258050.0906825356538702
(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) 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 1.00549 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 0.953 0.974 0.982 0.926
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
-0.47 0.0478 0.13 0.1891 0 0.6022 DNA recombination; repair and maintenance (4hpi)
(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
4XW3 X-ray 2.0Å A/B=72-283.

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

HIV Partner Interaction Type PubMed
Tat enhances 25496916
Rev binds 25496916
Rev relocalized by 15892970
15892970
16354571
Gag-Pol complexes with 23125841
capsid downregulated by 25496916
HIV-1 virus replication enhanced by expression of human gene 22051512
Nef complexes with 23125841
Tat interacts with 25496916
25496916
Rev interacts with 15567440
17661632
18508616
19149558
21358275
21763499
22051512
2360815715567440
1914955821763499
22051512
22174317
25496916
Envelope surface glycoprotein gp120 complexes with 23125841
Pr55(Gag) complexes with 23125841
Rev co-localizes with 23608157
Tat binds 25496916

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found
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