Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000774
UniProt IDQ9NR30
Primary gene name(s)DDX21
Synonym gene name(s)unknown
Protein nameNucleolar RNA helicase 2
Protein functionRNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase, Pol I and II: promotes ribosomal RNA, rRNA processing and transcription from polymerase II, Pol II, PubMed:25470060. Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs, PubMed:25470060. In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes, PubMed:25470060, PubMed:25477391. In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes, PubMed:25470060. Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77', PubMed:11823437, PubMed:25260534. Can unwind double-stranded RNA, helicase and can fold or introduce a secondary structure to a single-stranded RNA, foldase, PubMed:9461305. Involved in rRNA processing, PubMed:14559904, PubMed:18180292. {ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:14559904, ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:25260534, ECO:0000269|PubMed:25470060, ECO:0000269|PubMed:25477391, ECO:0000269|PubMed:9461305}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:23848194, ECO:0000269|PubMed:25260534, ECO:0000269|PubMed:25470060, ECO:0000269|PubMed:8614622}. Nucleus, nucleoplasm {ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:25260534, ECO:0000269|PubMed:25470060}. Note=Present both in nucleolus and nucleoplasm. Interaction with JUN promotes translocation from the nucleolus to the nucleoplasm, PubMed:11823437, PubMed:18180292. Interaction with WDR46 is required for localization to the nucleolus, PubMed:23848194. {ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:23848194}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9NR30
Gene Ontology
(Biological Process)
Complete annatation
osteoblast differentiation [GO:0001649];
positive regulation of gene expression, epigenetic [GO:0045815];
response to exogenous dsRNA [GO:0043330];
response to virus [GO:0009615];
RNA secondary structure unwinding [GO:0010501];
rRNA processing [GO:0006364];
transcription from RNA polymerase II promoter [GO:0006366]
Gene Ontology
(Molecular Function)
Complete annatation
7SK snRNA binding [GO:0097322];
ATP binding [GO:0005524];
ATP-dependent RNA helicase activity [GO:0004004];
double-stranded RNA binding [GO:0003725];
poly(A RNA binding [GO:0044822];
rRNA binding [GO:0019843];
snoRNA binding [GO:0030515]
Gene Ontology
(Cellular Component)
Complete annatation
membrane [GO:0016020];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction114625
Phylogenetic treeQ9NR30
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. CD32.148548211305423.21227711097549e-105.11791127025609e-09
AZA vs. DISU-0.1139846360405290.6515579518618130.960057478314726
AZA vs. IL70.6349895086700770.006509423767708580.257523738715673
AZA vs. SAHA-0.3183127645262690.1916008406420860.558373973325112
DISU vs. CD3-2.275275257330182.11064510313719e-093.89423063460098e-08
DISU vs. IL70.7403596503567590.003390094090490070.0597958280643232
DISU vs. SAHA-0.2036050981533670.4843479663786680.814657460203633
DMSO vs. AZA-0.008494751314047240.9594058682032361
DMSO vs. CD3-2.169046906070098.51687609326746e-111.35344660701555e-09
DMSO vs. DISU0.1035397903066410.6706454453334060.954355699827613
DMSO vs. IL70.6508398585021530.00248919951566440.0969630043892527
DMSO vs. SAHA-0.3169505272093010.1783513264050260.510044182210653
HIV vs. Mock in Activation0.1100672275274110.8596564432996780.999983755607037
HIV vs. Mock in Latency-0.07601283383527980.6443236181010330.999834320637052
IL7 vs. CD3-1.504960390468035.2316442473721e-064.32802270804828e-05
SAHA vs. CD3-2.492108054090392.76705325319426e-116.56684921663583e-10
SAHA vs. IL7-0.9569510430075359.62518788746314e-050.00190657138259684
(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
-0.5106 0.02597

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 -0.981029571
(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 0.402782 0.00199466
(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
0.954 1.016 0.663 0.491 0.713
(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
2M3D NMR - A=617-710.

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

HIV Partner Interaction Type PubMed
Rev interacts with 23608157
Rev enhanced by 23608157
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Pr55(Gag) complexes with 23125841
Tat interacts with 19454010
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found
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