Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001342
UniProt IDO15347
Primary gene name(s)HMGB3
Synonym gene name(s)HMG2A, HMG4
Protein nameHigh mobility group protein B3
Protein functionMultifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. Associates with chromatin and binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters, By similarity. Proposed to be involved in the innate immune response to nucleic acids by acting as a cytoplasmic promiscuous immunogenic DNA/RNA sensor, By similarity. Negatively regulates B-cell and myeloid cell differentiation. In hematopoietic stem cells may regulate the balance between self-renewal and differentiation. Involved in negative regulation of canonical Wnt signaling, By similarity. {ECO:0000250|UniProtKB:O54879, ECO:0000250|UniProtKB:P09429, ECO:0000250|UniProtKB:P40618}.
Subcellular locationNucleus {ECO:0000250|UniProtKB:P40618, ECO:0000255|PROSITE-ProRule:PRU00267}. Chromosome {ECO:0000305}. Cytoplasm {ECO:0000250|UniProtKB:O54879}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O15347
Gene Ontology
(Biological Process)
Complete annatation
DNA geometric change [GO:0032392];
DNA recombination [GO:0006310];
innate immune response [GO:0045087];
multicellular organism development [GO:0007275];
negative regulation of B cell differentiation [GO:0045578];
negative regulation of myeloid cell differentiation [GO:0045638];
regulation of transcription, DNA-templated [GO:0006355];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding, bending [GO:0008301];
double-stranded DNA binding [GO:0003690];
four-way junction DNA binding [GO:0000400];
poly(A RNA binding [GO:0044822]
Gene Ontology
(Cellular Component)
Complete annatation
chromosome [GO:0005694];
cytoplasm [GO:0005737];
nucleus [GO:0005634]
Protein-protein interaction109392
Phylogenetic treeO15347
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. CD31.812830542692759.46376730981413e-077.37527926026466e-06
AZA vs. DISU-0.1078419610110240.7662816662703990.976021571236163
AZA vs. IL70.112544235412030.7867863687373590.999311006273513
AZA vs. SAHA-0.02715852049094250.9372990772685620.986599683266836
DISU vs. CD3-1.933090170849552.92276270852376e-073.19490392083301e-06
DISU vs. IL70.2102879796766240.5061952823667310.830044367655729
DISU vs. SAHA0.08259928425648580.7836908450077290.941340936089223
DMSO vs. AZA-0.08364161912150760.8475082385603011
DMSO vs. CD3-1.906272614096945.01830428323302e-084.63523936400401e-07
DMSO vs. DISU0.02236435087372820.9471689686871660.993012243712903
DMSO vs. IL70.2032606143732720.607454019482210.913708218959648
DMSO vs. SAHA0.04934315217669340.8758212518066410.969166253985955
HIV vs. Mock in Activation0.1822366237512080.7701046308335480.999983755607037
HIV vs. Mock in Latency0.06869841943936140.8602248270355090.999834320637052
IL7 vs. CD3-1.693584041980253.55068970003813e-073.82138081320413e-06
SAHA vs. CD3-1.86401442784154.76610671595878e-074.18805995390664e-06
SAHA vs. IL7-0.1415473618646490.6306277753373110.816892769593663
(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 0.284292 0.0366958
(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
1.036 0.981 0.916 0.89 1.148
(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
203744_at 1.91 No upregulated in CD8+ cells

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
2EQZ NMR - A=1-79.
2YQI NMR - A=91-164.

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found