Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001409
UniProt IDP38935
Primary gene name(s)IGHMBP2
Synonym gene name(s)SMBP2, SMUBP2
Protein nameDNA-binding protein SMUBP-2
Protein function5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation, By similarity. DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV. {ECO:0000250, ECO:0000269|PubMed:19158098, ECO:0000269|PubMed:19299493}.
Subcellular locationNucleus {ECO:0000269|PubMed:19299493}. Cytoplasm {ECO:0000269|PubMed:19299493}. Cell projection, axon {ECO:0000250}. Note=Colocalizes with the translation initiation factor EIF4G2. {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P38935
Gene Ontology
(Biological Process)
Complete annatation
DNA recombination [GO:0006310];
DNA repair [GO:0006281];
DNA replication [GO:0006260];
protein homooligomerization [GO:0051260];
regulation of transcription from RNA polymerase II promoter [GO:0006357];
transcription, DNA-templated [GO:0006351];
translation [GO:0006412]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
ATP-dependent 5'-3' DNA helicase activity [GO:0043141];
ATP-dependent 5'-3' RNA helicase activity [GO:0032575];
DNA binding [GO:0003677];
DNA-dependent ATPase activity [GO:0008094];
DNA helicase activity [GO:0003678];
ribosome binding [GO:0043022];
RNA binding [GO:0003723];
RNA-dependent ATPase activity [GO:0008186];
single-stranded DNA binding [GO:0003697];
transcription factor binding [GO:0008134];
tRNA binding [GO:0000049];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
axon [GO:0030424];
cytoplasm [GO:0005737];
growth cone [GO:0030426];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nucleus [GO:0005634]
Protein-protein interaction109728
Phylogenetic treeP38935
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      Yes
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. CD30.1772765764701610.5899001728142450.696184747056323
AZA vs. DISU0.02770694524513210.9132257295462010.994271142470137
AZA vs. IL7-0.243138262254170.2118361136710430.977106618390875
AZA vs. SAHA-0.160422713468990.514598180747490.830519590641078
DISU vs. CD3-0.1624633892861780.6552158344654250.7547498351618
DISU vs. IL7-0.2803221462234950.2687580399968180.655268874810291
DISU vs. SAHA-0.1859884148405110.5255748680089330.839187573961102
DMSO vs. AZA0.06081271890720050.720618397181581
DMSO vs. CD3-0.1307996152111690.6840271584943080.767187994544129
DMSO vs. DISU0.03053859540058390.9008744052362080.988283279918411
DMSO vs. IL7-0.2962559257886720.1039242088136120.584355631430512
DMSO vs. SAHA-0.2261849120362660.3412024652589650.693681688104392
HIV vs. Mock in Activation0.1370372861017820.8261509660490370.999983755607037
HIV vs. Mock in Latency0.09460575125358030.5720427449236340.999834320637052
IL7 vs. CD3-0.4143957765576950.2004495949421190.32296918701898
SAHA vs. CD3-0.3615298735975950.3112619382240520.424845340914451
SAHA vs. IL70.0794467910404740.7462357697694020.885098822359233
(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) TRUE
(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 0.319991 0.024828
(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
0.995 1.359 1.242 0.845 1.173
(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
1MSZ NMR - A=711-786.
2LRR NMR - A=711-786.
4B3F X-ray 2.5Å X=3-648.
4B3G X-ray 2.8Å A/B=3-648.

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

HIV Partner Interaction Type PubMed
HIV-1 virus replication enhanced by expression of human gene 18187620

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found
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