Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002254
UniProt IDO15514
Primary gene name(s)POLR2D
Synonym gene name(s)unknown
Protein nameDNA-directed RNA polymerase II subunit RPB4
Protein functionDNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA, By similarity. {ECO:0000250, ECO:0000269|PubMed:9852112}.
Subcellular locationNucleus {ECO:0000269|PubMed:9852112}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O15514
Gene Ontology
(Biological Process)
Complete annatation
7-methylguanosine mRNA capping [GO:0006370];
fibroblast growth factor receptor signaling pathway [GO:0008543];
gene expression [GO:0010467];
gene silencing by RNA [GO:0031047];
mRNA export from nucleus in response to heat stress [GO:0031990];
mRNA splicing, via spliceosome [GO:0000398];
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay [GO:0000288];
positive regulation of translational initiation [GO:0045948];
positive regulation of viral transcription [GO:0050434];
recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex [GO:0034402];
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-directed RNA polymerase activity [GO:0003899];
nucleotide binding [GO:0000166];
translation initiation factor binding [GO:0031369]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasmic mRNA processing body [GO:0000932];
DNA-directed RNA polymerase II, core complex [GO:0005665];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction111429
Phylogenetic treeO15514
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. CD31.779406257978531.38028397711487e-071.28894920093404e-06
AZA vs. DISU-0.113151258946910.656837296589970.960426582104957
AZA vs. IL70.279056204413650.1515412068451860.919682784157423
AZA vs. SAHA-0.1911713641193390.4373058278716860.786253345579412
DISU vs. CD3-1.904903373313393.76544952662705e-074.01133471126333e-06
DISU vs. IL70.383205838431360.1307795503282240.473676742044305
DISU vs. SAHA-0.07696449205534420.7927114903789670.944722036335711
DMSO vs. AZA-0.08096872686884190.6351418304918521
DMSO vs. CD3-1.871944622256521.52074489667697e-081.56627916616247e-07
DMSO vs. DISU0.03034523138567170.9016929798374820.988283279918411
DMSO vs. IL70.3670872276358940.04397315982833730.422755155027874
DMSO vs. SAHA-0.1171337102686940.6222824833640320.876405878588854
HIV vs. Mock in Activation-0.03362984130022290.9568671174659620.999983755607037
HIV vs. Mock in Latency-0.006766890211279480.9678210762831130.999834320637052
IL7 vs. CD3-1.49206434439845.51118394809258e-064.52697959943321e-05
SAHA vs. CD3-1.995804496158015.37740248995888e-086.04757130773734e-07
SAHA vs. IL7-0.4738676410454590.05380794466761830.193549600212914
(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 0.140462 0.353433
(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
0.975 1.047 1.015 0.901 1.069
(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
2C35 X-ray 2.7Å A/C/E/G=1-142.
5IY6 EM 7.2Å D=1-142.
5IY7 EM 8.6Å D=1-142.
5IY8 EM 7.9Å D=1-142.
5IY9 EM 6.3Å D=1-142.
5IYA EM 5.4Å D=1-142.
5IYB EM 3.9Å D=1-142.
5IYC EM 3.9Å D=1-142.
5IYD EM 3.9Å D=1-142.

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)
hsa05169 Epstein-Barr virus infection - Homo sapiens (human)