Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001341
UniProt IDP26583
Primary gene name(s)HMGB2
Synonym gene name(s)HMG2
Protein nameHigh mobility group protein B2
Protein functionMultifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. In the nucleus is an abundant chromatin-associated non-histone protein involved in transcription, chromatin remodeling and V(DJ recombination and probably other processes. 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 enhancing transcription factor binding and/or bringing distant regulatory sequences into close proximity, PubMed:7797075, PubMed:11909973, PubMed:19522541, PubMed:18413230, PubMed:19965638, PubMed:20123072. Involved in V(DJ recombination by acting as a cofactor of the RAG complex: acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences, RSS, By similarity. Proposed to be involved in the innate immune response to nucleic acids by acting as a promiscuous immunogenic DNA/RNA sensor which cooperates with subsequent discriminative sensing by specific pattern recognition receptors, By similarity. In the extracellular compartment acts as a chemokine. Promotes proliferation and migration of endothelial cells implicating AGER/RAGE, PubMed:19811285. Has antimicrobial activity in gastrointestinal epithelial tissues, PubMed:23877675. Involved in inflammatory response to antigenic stimulus coupled with proinflammatory activity, By similarity. Involved in modulation of neurogenesis probably by regulation of neural stem proliferation, By similarity. Involved in articular cartilage surface maintenance implicating LEF1 and the Wnt/beta-catenin pathway, By similarity. {ECO:0000250|UniProtKB:P09429, ECO:0000250|UniProtKB:P30681, ECO:0000269|PubMed:11909973, ECO:0000269|PubMed:18413230, ECO:0000269|PubMed:19522541, ECO:0000269|PubMed:19811285, ECO:0000269|PubMed:19965638, ECO:0000269|PubMed:23877675, ECO:0000269|PubMed:7797075, ECO:0000305|PubMed:20123072}.
Subcellular locationNucleus {ECO:0000269|PubMed:11909973, ECO:0000269|PubMed:12925773, ECO:0000269|PubMed:23877675}. Chromosome {ECO:0000269|PubMed:12925773}. Cytoplasm {ECO:0000269|PubMed:11909973, ECO:0000269|PubMed:23877675}. Secreted {ECO:0000269|PubMed:19811285, ECO:0000269|PubMed:23877675}. Note=In basal state predominantly nuclear. {ECO:0000305}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P26583
Gene Ontology
(Biological Process)
Complete annatation
apoptotic DNA fragmentation [GO:0006309];
cell chemotaxis [GO:0060326];
cellular response to lipopolysaccharide [GO:0071222];
chromatin organization [GO:0006325];
defense response to Gram-negative bacterium [GO:0050829];
defense response to Gram-positive bacterium [GO:0050830];
DNA geometric change [GO:0032392];
DNA ligation involved in DNA repair [GO:0051103];
DNA topological change [GO:0006265];
inflammatory response to antigenic stimulus [GO:0002437];
innate immune response [GO:0045087];
male gonad development [GO:0008584];
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors [GO:1902042];
negative regulation of transcription, DNA-templated [GO:0045892];
nucleosome assembly [GO:0006334];
positive regulation of DNA binding [GO:0043388];
positive regulation of endothelial cell proliferation [GO:0001938];
positive regulation of erythrocyte differentiation [GO:0045648];
positive regulation of innate immune response [GO:0045089];
positive regulation of interferon-beta production [GO:0032728];
positive regulation of megakaryocyte differentiation [GO:0045654];
positive regulation of nuclease activity [GO:0032075];
positive regulation of transcription, DNA-templated [GO:0045893];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
regulation of neurogenesis [GO:0050767];
regulation of stem cell proliferation [GO:0072091];
regulation of transcription from RNA polymerase II promoter [GO:0006357];
response to drug [GO:0042493];
response to lipopolysaccharide [GO:0032496];
response to steroid hormone [GO:0048545];
spermatid nucleus differentiation [GO:0007289];
transcription, DNA-templated [GO:0006351];
V(DJ recombination [GO:0033151]
Gene Ontology
(Molecular Function)
Complete annatation
chemoattractant activity [GO:0042056];
damaged DNA binding [GO:0003684];
DNA binding [GO:0003677];
DNA binding, bending [GO:0008301];
double-stranded DNA binding [GO:0003690];
drug binding [GO:0008144];
enhancer sequence-specific DNA binding [GO:0001158];
four-way junction DNA binding [GO:0000400];
non-sequence-specific DNA binding, bending [GO:0044378];
poly(A RNA binding [GO:0044822];
RAGE receptor binding [GO:0050786];
single-stranded DNA binding [GO:0003697];
supercoiled DNA binding [GO:0097100];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
transcription factor binding [GO:0008134];
transcription regulatory region DNA binding [GO:0044212]
Gene Ontology
(Cellular Component)
Complete annatation
cell [GO:0005623];
condensed chromosome [GO:0000793];
cytoplasm [GO:0005737];
extracellular space [GO:0005615];
nuclear chromatin [GO:0000790];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
perinuclear region of cytoplasm [GO:0048471];
protein complex [GO:0043234]
Protein-protein interaction109391
Phylogenetic treeP26583
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. CD3-0.3256483260786020.6673773740056770.759205357461965
AZA vs. DISU0.1093086181019620.6653570750620690.962109385105098
AZA vs. IL7-0.02420648818553380.9256131429882270.999311006273513
AZA vs. SAHA-0.09139691464461950.7083007238952570.917734666666417
DISU vs. CD30.4221582701775870.5719261749034320.688210677775552
DISU vs. IL7-0.1424736959789220.5788836895345920.866428874080022
DISU vs. SAHA-0.2003065614696210.493411542390820.82013955612353
DMSO vs. AZA-0.1089276554245160.5152880376243751
DMSO vs. CD30.2028193509557040.788970789394390.850873000374149
DMSO vs. DISU-0.2209369295279660.3654943520162930.850082323454514
DMSO vs. IL70.09215986799696710.6943765197005480.936954851917814
DMSO vs. SAHA0.01026380620040350.9652660533697750.992417492274894
HIV vs. Mock in Activation-0.1016899373940080.9469356254904120.999983755607037
HIV vs. Mock in Latency0.06958260294036010.7970342162356120.999834320637052
IL7 vs. CD30.310601514673720.6822915806491540.783556647247596
SAHA vs. CD30.2082751392145810.7896060093645770.850379658480967
SAHA vs. IL7-0.07158025646516370.7718019004771950.899393372312791
(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
1.8 0.009504517 1.4 0.077013931 1.4 0.075068843
(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 0.478266 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
1.078 0.878 0.835 0.853 0.833
(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
208808_s_at 1.5 No upregulated in CD8+ cells

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

not found

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
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