Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002252
UniProt IDP24928
Primary gene name(s)POLR2A
Synonym gene name(s)POLR2
Protein nameDNA-directed RNA polymerase II subunit RPB1
Protein functionDNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single-stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain, CTD of Pol II largest subunit, RPB1, which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Acts as an RNA-dependent RNA polymerase when associated with small delta antigen of Hepatitis delta virus, acting both as a replicate and transcriptase for the viral RNA circular genome. {ECO:0000269|PubMed:18032511, ECO:0000269|PubMed:20231364, ECO:0000269|PubMed:23748380, ECO:0000269|PubMed:9852112}.
Subcellular locationNucleus {ECO:0000269|PubMed:9852112}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P24928
Gene Ontology
(Biological Process)
Complete annatation
7-methylguanosine mRNA capping [GO:0006370];
DNA-templated transcription, termination [GO:0006353];
fibroblast growth factor receptor signaling pathway [GO:0008543];
gene expression [GO:0010467];
gene silencing by RNA [GO:0031047];
mRNA splicing, via spliceosome [GO:0000398];
positive regulation of RNA splicing [GO:0033120];
positive regulation of viral transcription [GO:0050434];
regulation of transcription, DNA-templated [GO:0006355];
snRNA transcription from RNA polymerase II promoter [GO:0042795];
somatic stem cell population maintenance [GO:0035019];
transcription-coupled nucleotide-excision repair [GO:0006283];
transcription elongation from RNA polymerase II promoter [GO:0006368];
transcription from RNA polymerase II promoter [GO:0006366];
transcription initiation from RNA polymerase II promoter [GO:0006367]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
DNA-directed RNA polymerase activity [GO:0003899];
metal ion binding [GO:0046872];
poly(A RNA binding [GO:0044822];
RNA-directed RNA polymerase activity [GO:0003968];
ubiquitin protein ligase binding [GO:0031625]
Gene Ontology
(Cellular Component)
Complete annatation
DNA-directed RNA polymerase II, core complex [GO:0005665];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction111426
Phylogenetic treeP24928
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. CD30.3514738601965170.2826905917571230.398868432780693
AZA vs. DISU-0.008740904162433020.9724028287425540.997811953897277
AZA vs. IL7-0.02815680837417520.8833041093950490.999311006273513
AZA vs. SAHA-0.1886838189791010.4385661259854290.786651023474113
DISU vs. CD3-0.3729083176757890.3037516733294260.435224852609018
DISU vs. IL7-0.02907706212270180.9082343578139450.982189124739072
DISU vs. SAHA-0.1772548844820660.542353071564580.846850719182531
DMSO vs. AZA0.1133999086492280.4970732976723791
DMSO vs. CD3-0.2491255373481020.4353823508441210.54865372663924
DMSO vs. DISU0.1204080333500090.6218023156278070.942807213654396
DMSO vs. IL7-0.1342267554264340.4540677565961270.870758796926069
DMSO vs. SAHA-0.3075326853225520.1921452024543930.52778791276357
HIV vs. Mock in Activation0.6543566093079760.2945844883195910.999983755607037
HIV vs. Mock in Latency0.1471195930375450.3711171336926030.999834320637052
IL7 vs. CD3-0.3746337370442740.2435822390673790.373995628956158
SAHA vs. CD3-0.5633675806224250.1113889186361870.190126968382301
SAHA vs. IL7-0.1632002861928240.5030249435198950.730894584205205
(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 0.019021 0.926669
(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
1.043 0.901 0.796 0.767 0.961
(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
2GHQ X-ray 2.0Å C/D=1795-1803.
2GHT X-ray 1.8Å C/D=1796-1803.
2LTO NMR - B=1804-1816.
3D9K X-ray 2.2Å Y/Z=1790-1803.
3D9L X-ray 2.2Å Y/Z=1790-1803.
3D9M X-ray 1.7Å Y/Z=1790-1803.
3D9N X-ray 1.6Å Y/Z=1790-1803.
3D9O X-ray 2.0Å Z=1790-1803.
3D9P X-ray 2.1Å Y/Z=1790-1803.
4JXT X-ray 1.9Å B=1787-1805.
5IY6 EM 7.2Å A=1-1970.
5IY7 EM 8.6Å A=1-1970.
5IY8 EM 7.9Å A=1-1970.
5IY9 EM 6.3Å A=1-1970.
5IYA EM 5.4Å A=1-1970.
5IYB EM 3.9Å A=1-1970.
5IYC EM 3.9Å A=1-1970.
5IYD EM 3.9Å A=1-1970.

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

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa00230 Purine metabolism - Homo sapiens (human)
hsa00240 Pyrimidine metabolism - Homo sapiens (human)
hsa01100 Metabolic pathways - Homo sapiens (human)
hsa03020 RNA polymerase - Homo sapiens (human)
hsa05016 Huntington's disease - Homo sapiens (human)
hsa05168 Herpes simplex infection - Homo sapiens (human)
hsa05169 Epstein-Barr virus infection - Homo sapiens (human)