Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001913
UniProt IDP19338
Primary gene name(s)NCL
Synonym gene name(s)unknown
Protein nameNucleolin
Protein functionNucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. {ECO:0000269|PubMed:10393184}.
Subcellular locationNucleus, nucleolus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P19338
Gene Ontology
(Biological Process)
Complete annatation
angiogenesis [GO:0001525];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter [GO:1901838]
Gene Ontology
(Molecular Function)
Complete annatation
calcium ion binding [GO:0005509];
identical protein binding [GO:0042802];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
protein C-terminus binding [GO:0008022];
RNA binding [GO:0003723];
rRNA primary transcript binding [GO:0042134];
selenocysteine insertion sequence binding [GO:0035368];
single-stranded DNA binding [GO:0003697];
telomeric DNA binding [GO:0042162]
Gene Ontology
(Cellular Component)
Complete annatation
cell cortex [GO:0005938];
cell surface [GO:0009986];
cytoplasmic ribonucleoprotein granule [GO:0036464];
dense fibrillar component [GO:0001651];
extracellular exosome [GO:0070062];
fibrillar center [GO:0001650];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction110771
Phylogenetic treeP19338
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. CD32.026436429299932.33466745935829e-093.10849010136467e-08
AZA vs. DISU-0.1913852219602440.4487717149350420.918669250520452
AZA vs. IL70.433610970802440.0237560258675750.491596466916618
AZA vs. SAHA-0.5793073521345660.01807665492784020.143868794288417
DISU vs. CD3-2.229665181553054.11951295298252e-097.09686151465811e-08
DISU vs. IL70.6158763160686150.01474275036367970.148660175071887
DISU vs. SAHA-0.3870113758922990.1840347074615670.550424107194537
DMSO vs. AZA-0.03108776450560820.8519896489858681
DMSO vs. CD3-2.06695157188424.70758432236096e-106.47669021154044e-09
DMSO vs. DISU0.1589530976756740.5141308945114260.912382545959396
DMSO vs. IL70.4717207088948490.008552088486121770.191849306440901
DMSO vs. SAHA-0.555879512272480.01882716896830990.136463582338732
HIV vs. Mock in Activation0.02335153437934740.9700299621852410.999983755607037
HIV vs. Mock in Latency-0.005046156010270460.9755110774780040.999834320637052
IL7 vs. CD3-1.584854681447361.37896211138688e-061.3072387361594e-05
SAHA vs. CD3-2.630492804449282.73736588951579e-127.79812929206104e-11
SAHA vs. IL7-1.016138683571063.68562637342862e-050.000872168476500204
(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
-0.4312 0.02841

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 -1.359513938
(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
-1.9 0.063741592 -2.1 0.027884346 -2.1 0.082497889
(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 1.7901 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
1.03 0.976 0.847 0.77 0.897
(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
2FC8 NMR - A=564-652.
2FC9 NMR - A=478-565.
2KRR NMR - A=300-466.

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

HIV Partner Interaction Type PubMed
matrix fractionates with 12027446
14978336
reverse transcriptase fractionates with 12027446
Pr55(Gag) upregulates 24690621
Pr55(Gag) binds 14978336
nucleocapsid downregulates 19884766
Envelope surface glycoprotein gp120 downregulates 19492063
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Pr55(Gag) complexes with 23125841
24690621
Tat downregulates 19884766
Pr55(Gag) fractionates with 12027446
14978336
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa05130 Pathogenic Escherichia coli infection - Homo sapiens (human)
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