Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002193
UniProt IDQ13563
Primary gene name(s)PKD2
Synonym gene name(s)TRPP2
Protein namePolycystin-2
Protein functionFunctions as a calcium permeable cation channel involved in fluid-flow mechanosensation by the primary cilium in renal epithelium. Together with TRPV4, forms mechano- and thermosensitive channels in cilium, PubMed:18695040. PKD1 and PKD2 may function through a common signaling pathway that is necessary for normal tubulogenesis. Acts as a regulator of cilium length, together with PKD1. The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling. Also involved in left/right axis specification downstream of nodal flow: forms a complex with PKD1L1 in cilia to facilitate flow detection in left/right patterning, By similarity. {ECO:0000250|UniProtKB:O35245, ECO:0000269|PubMed:18695040}.
Subcellular locationCell projection, cilium membrane {ECO:0000269|PubMed:18695040, ECO:0000269|PubMed:27259053};
Multi-pass membrane protein {ECO:0000255}. Endoplasmic reticulum {ECO:0000269|PubMed:10760273}. Cell membrane {ECO:0000269|PubMed:27259053}. Note=Cell surface and cilium localization requires GANAB. {ECO:0000269|PubMed:27259053}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q13563
Gene Ontology
(Biological Process)
Complete annatation
aorta development [GO:0035904];
branching involved in ureteric bud morphogenesis [GO:0001658];
calcium ion transmembrane transport [GO:0070588];
calcium ion transport [GO:0006816];
cell cycle arrest [GO:0007050];
cellular response to fluid shear stress [GO:0071498];
cellular response to hydrostatic pressure [GO:0071464];
cellular response to osmotic stress [GO:0071470];
cellular response to reactive oxygen species [GO:0034614];
centrosome duplication [GO:0051298];
cytoplasmic sequestering of transcription factor [GO:0042994];
detection of mechanical stimulus [GO:0050982];
detection of nodal flow [GO:0003127];
determination of left/right symmetry [GO:0007368];
determination of liver left/right asymmetry [GO:0071910];
embryonic placenta development [GO:0001892];
heart development [GO:0007507];
heart looping [GO:0001947];
JAK-STAT cascade [GO:0007259];
liver development [GO:0001889];
mesonephric duct development [GO:0072177];
mesonephric tubule development [GO:0072164];
metanephric ascending thin limb development [GO:0072218];
metanephric cortex development [GO:0072214];
metanephric cortical collecting duct development [GO:0072219];
metanephric distal tubule development [GO:0072235];
metanephric mesenchyme development [GO:0072075];
metanephric part of ureteric bud development [GO:0035502];
metanephric smooth muscle tissue development [GO:0072208];
metanephric S-shaped body morphogenesis [GO:0072284];
negative regulation of cell proliferation [GO:0008285];
negative regulation of G1/S transition of mitotic cell cycle [GO:2000134];
negative regulation of ryanodine-sensitive calcium-release channel activity [GO:0060315];
neural tube development [GO:0021915];
placenta blood vessel development [GO:0060674];
positive regulation of cell cycle arrest [GO:0071158];
positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle [GO:0031659];
positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity [GO:0031587];
positive regulation of nitric oxide biosynthetic process [GO:0045429];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
regulation of calcium ion import [GO:0090279];
regulation of cAMP metabolic process [GO:0030814];
regulation of cell proliferation [GO:0042127];
release of sequestered calcium ion into cytosol [GO:0051209];
renal artery morphogenesis [GO:0061441];
renal tubule morphogenesis [GO:0061333];
sodium ion transmembrane transport [GO:0035725];
spinal cord development [GO:0021510]
Gene Ontology
(Molecular Function)
Complete annatation
actinin binding [GO:0042805];
ATPase binding [GO:0051117];
calcium-induced calcium release activity [GO:0048763];
calcium ion binding [GO:0005509];
cytoskeletal protein binding [GO:0008092];
HLH domain binding [GO:0043398];
identical protein binding [GO:0042802];
ion channel binding [GO:0044325];
phosphoprotein binding [GO:0051219];
potassium channel activity [GO:0005267];
protein homodimerization activity [GO:0042803];
receptor binding [GO:0005102];
voltage-gated calcium channel activity [GO:0005245];
voltage-gated cation channel activity [GO:0022843];
voltage-gated ion channel activity [GO:0005244];
voltage-gated sodium channel activity [GO:0005248]
Gene Ontology
(Cellular Component)
Complete annatation
basal cortex [GO:0045180];
basal plasma membrane [GO:0009925];
cell-cell junction [GO:0005911];
ciliary basal body [GO:0036064];
ciliary membrane [GO:0060170];
cilium [GO:0005929];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
endoplasmic reticulum [GO:0005783];
endoplasmic reticulum membrane [GO:0005789];
extracellular exosome [GO:0070062];
integral component of cytoplasmic side of endoplasmic reticulum membrane [GO:0071458];
integral component of lumenal side of endoplasmic reticulum membrane [GO:0071556];
integral component of plasma membrane [GO:0005887];
lamellipodium [GO:0030027];
mitotic spindle [GO:0072686];
motile primary cilium [GO:0031512];
nonmotile primary cilium [GO:0031513];
plasma membrane [GO:0005886];
polycystin complex [GO:0002133]
Protein-protein interaction111328
Phylogenetic treeQ13563
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. CD30.2550008514291610.4407565911660630.562068139610365
AZA vs. DISU-0.2766540438045950.2791388356342110.849533375398768
AZA vs. IL70.1012449325548380.6020945393856890.999311006273513
AZA vs. SAHA0.3385472562220430.1696713036003040.525611432484789
DISU vs. CD3-0.5438679485504760.1351863904720980.236321425255295
DISU vs. IL70.3693211699010910.1473926569695250.500122141875431
DISU vs. SAHA0.6160385686780860.03886607551822710.241856921237506
DMSO vs. AZA-0.08047927422200830.6360230881791221
DMSO vs. CD3-0.3461653518911740.2848283547270630.394061820549472
DMSO vs. DISU0.1946791648663360.4302634980729770.881718877024027
DMSO vs. IL70.1889029155737010.2986859737415720.78444095020108
DMSO vs. SAHA0.4116088013639580.08385019974160880.337618584105206
HIV vs. Mock in Activation0.03860470718965290.9506442053758630.999983755607037
HIV vs. Mock in Latency-0.1097208829823010.5096428901737060.999834320637052
IL7 vs. CD3-0.1454622416174410.6541810180357180.762139674979968
SAHA vs. CD30.05803790489410140.8726926896510250.911019592202892
SAHA vs. IL70.2333660021487790.3418535517083930.591290928106979
(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 0.412411 0.00657227
(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
unknown unknown unknown unknown unknown
(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
2KLD NMR - A=680-796.
2KLE NMR - A=680-796.
2KQ6 NMR - A=720-797.
2Y4Q NMR - A=717-792.
3HRN X-ray 1.9Å A=833-895.
3HRO X-ray 1.9Å A=833-872.
5K47 EM 4.2Å A/B/C/D=185-723.

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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