Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001996
UniProt IDP06748
Primary gene name(s)NPM1
Synonym gene name(s)NPM
Protein nameNucleophosmin
Protein functionInvolved in diverse cellular processes such as ribosome biogenesis, centrosome duplication, protein chaperoning, histone assembly, cell proliferation, and regulation of tumor suppressors p53/TP53 and ARF. Binds ribosome presumably to drive ribosome nuclear export. Associated with nucleolar ribonucleoprotein structures and bind single-stranded nucleic acids. Acts as a chaperonin for the core histones H3, H2B and H4. Stimulates APEX1 endonuclease activity on apurinic/apyrimidinic, AP double-stranded DNA but inhibits APEX1 endonuclease activity on AP single-stranded RNA. May exert a control of APEX1 endonuclease activity within nucleoli devoted to repair AP on rDNA and the removal of oxidized rRNA molecules. In concert with BRCA2, regulates centrosome duplication. Regulates centriole duplication: phosphorylation by PLK2 is able to trigger centriole replication. Negatively regulates the activation of EIF2AK2/PKR and suppresses apoptosis through inhibition of EIF2AK2/PKR autophosphorylation. Antagonizes the inhibitory effect of ATF5 on cell proliferation and relieves ATF5-induced G2/M blockade, PubMed:22528486. {ECO:0000269|PubMed:12882984, ECO:0000269|PubMed:16107701, ECO:0000269|PubMed:17015463, ECO:0000269|PubMed:18809582, ECO:0000269|PubMed:19188445, ECO:0000269|PubMed:20352051, ECO:0000269|PubMed:21084279, ECO:0000269|PubMed:22002061, ECO:0000269|PubMed:22528486}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:22528486}. Nucleus, nucleoplasm. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Generally nucleolar, but is translocated to the nucleoplasm in case of serum starvation or treatment with anticancer drugs. Has been found in the cytoplasm in patients with primary acute myelogenous leukemia, AML, but not with secondary AML. Can shuttle between cytoplasm and nucleus. Co- localizes with the methylated form of RPS10 in the granular component, GC region of the nucleolus. Colocalized with nucleolin and APEX1 in nucleoli. Isoform 1 of NEK2 is required for its localization to the centrosome during mitosis.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P06748
Gene Ontology
(Biological Process)
Complete annatation
cell aging [GO:0007569];
CENP-A containing nucleosome assembly [GO:0034080];
centrosome cycle [GO:0007098];
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest [GO:0006977];
DNA repair [GO:0006281];
intracellular protein transport [GO:0006886];
negative regulation of apoptotic process [GO:0043066];
negative regulation of cell proliferation [GO:0008285];
negative regulation of centrosome duplication [GO:0010826];
negative regulation of protein kinase activity by regulation of protein phosphorylation [GO:0044387];
nucleocytoplasmic transport [GO:0006913];
nucleosome assembly [GO:0006334];
positive regulation of cell cycle G2/M phase transition [GO:1902751];
positive regulation of cell proliferation [GO:0008284];
positive regulation of NF-kappaB transcription factor activity [GO:0051092];
positive regulation of transcription, DNA-templated [GO:0045893];
positive regulation of translation [GO:0045727];
protein localization [GO:0008104];
protein oligomerization [GO:0051259];
regulation of centriole replication [GO:0046599];
regulation of eIF2 alpha phosphorylation by dsRNA [GO:0060735];
regulation of endodeoxyribonuclease activity [GO:0032071];
regulation of endoribonuclease activity [GO:0060699];
response to stress [GO:0006950];
ribosome assembly [GO:0042255];
signal transduction [GO:0007165];
viral process [GO:0016032]
Gene Ontology
(Molecular Function)
Complete annatation
histone binding [GO:0042393];
NF-kappaB binding [GO:0051059];
poly(A RNA binding [GO:0044822];
protein heterodimerization activity [GO:0046982];
protein homodimerization activity [GO:0042803];
protein kinase binding [GO:0019901];
protein kinase inhibitor activity [GO:0004860];
ribosomal large subunit binding [GO:0043023];
ribosomal small subunit binding [GO:0043024];
RNA binding [GO:0003723];
Tat protein binding [GO:0030957];
transcription coactivator activity [GO:0003713];
unfolded protein binding [GO:0051082]
Gene Ontology
(Cellular Component)
Complete annatation
centrosome [GO:0005813];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
focal adhesion [GO:0005925];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
spindle pole centrosome [GO:0031616]
Protein-protein interaction110929
Phylogenetic treeP06748
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. CD32.130446542080423.89586585214374e-106.08481762937933e-09
AZA vs. DISU-0.1325718216907790.5992579273602330.955158276076142
AZA vs. IL70.2449415973772980.2122855296889980.977106618390875
AZA vs. SAHA-0.05082316258198120.8344367792825380.960670942185365
DISU vs. CD3-2.275244754473231.91670612714745e-093.58825418099324e-08
DISU vs. IL70.368766876468940.1426185153566540.491919001767977
DISU vs. SAHA0.0819333197487650.7780976494417770.938587295880985
DMSO vs. AZA-0.1798456147365780.2805062894095011
DMSO vs. CD3-2.321931662131534.06519262696747e-127.96386565998244e-11
DMSO vs. DISU-0.04937244925065530.8392425744018810.982583769983649
DMSO vs. IL70.4321382150742770.01597339862795490.263168288870404
DMSO vs. SAHA0.1212058050976690.6060518433790360.867774549695606
HIV vs. Mock in Activation-0.1448977272182960.8155503024152710.999983755607037
HIV vs. Mock in Latency-0.07253292225214160.658525950604780.999834320637052
IL7 vs. CD3-1.876111660462151.45882048663282e-082.12452185459096e-07
SAHA vs. CD3-2.207083662256412.07699168974784e-093.24189888058595e-08
SAHA vs. IL7-0.2998831022307280.2171538882983190.455584928630323
(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
-0.4418 0.02219

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 -1.700671294
(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
1.7 0.000113617 1.2 0.039114775 1.2 0.306239443
(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 0.0195464 0.926363
(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
1.04 1.046 0.914 0.866 0.864
(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
2LLH NMR - A=225-294.
2P1B X-ray 2.7Å A/B/C/D/E/F/G/H/I/J=9-122.
2VXD NMR - A=243-294.

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

HIV Partner Interaction Type PubMed
Rev stimulated by 7794916
9092824
19149558
Rev binds 2017166
12511551
16354571
191495582109912
2404140
Gag-Pol complexes with 23125841
Tat complexes with 24316072
Tat upregulates 23364796
Tat activated by 21425800
21763502
Nef complexes with 23125841
Tat interacts with 25496916
Rev interacts with 22174317
7628555
8224012
9150888
Envelope surface glycoprotein gp120 complexes with 23125841
Vpr downregulates 23874603
Rev associates with 2109912
7593322
18775548
19149558
19339032
Pr55(Gag) complexes with 23125841
24690621
Rev co-localizes with 18775548
Tat binds 7826206
9094689
19454010
21763502
Tat regulated by 21763502

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found
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