Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002686
UniProt IDP63208
Primary gene name(s)SKP1
Synonym gene name(s)EMC19, OCP2, SKP1A, TCEB1L
Protein nameS-phase kinase-associated protein 1
Protein functionEssential component of the SCF, SKP1-CUL1-F-box protein ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as an adapter that links the F-box protein to CUL1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC and SCF(FBXW11 direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11 directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5, CEP68 and probably NFKB2, PubMed:25704143. SCF(SKP2 directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2 directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7 directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain, NICD, and probably PSEN1. SCF(FBXW2 directs ubiquitination of GCM1. SCF(FBXO32 directs ubiquitination of MYOD1. SCF(FBXO7 directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33 directs ubiquitination of YBX1. SCF(FBXO11 directs ubiquitination of BCL6 and DTL but does not seem to direct ubiquitination of TP53. SCF(BTRC mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(CCNF directs ubiquitination of CCP110. SCF(FBXL3 and SCF(FBXL21 direct ubiquitination of CRY1 and CRY2. SCF(FBXO9 directs ubiquitination of TTI1 and TELO2. SCF(FBXO10 directs ubiquitination of BCL2. {ECO:0000269|PubMed:16209941, ECO:0000269|PubMed:20181953, ECO:0000269|PubMed:22113614, ECO:0000269|PubMed:23431138, ECO:0000269|PubMed:25704143}.
Subcellular locationunknown
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P63208
Gene Ontology
(Biological Process)
Complete annatation
Fc-epsilon receptor signaling pathway [GO:0038095];
G2/M transition of mitotic cell cycle [GO:0000086];
histone H2A monoubiquitination [GO:0035518];
maintenance of protein location in nucleus [GO:0051457];
NIK/NF-kappaB signaling [GO:0038061];
positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition [GO:0051437];
proteasome-mediated ubiquitin-dependent protein catabolic process [GO:0043161];
protein polyubiquitination [GO:0000209];
protein ubiquitination [GO:0016567];
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process [GO:0031146];
stimulatory C-type lectin receptor signaling pathway [GO:0002223];
stress-activated MAPK cascade [GO:0051403];
T cell receptor signaling pathway [GO:0050852];
Wnt signaling pathway [GO:0016055]
Gene Ontology
(Molecular Function)
Complete annatation
beta-catenin binding [GO:0008013];
cullin family protein binding [GO:0097602];
ubiquitin-protein transferase activity [GO:0004842]
Gene Ontology
(Cellular Component)
Complete annatation
Cul7-RING ubiquitin ligase complex [GO:0031467];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
extracellular exosome [GO:0070062];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
SCF ubiquitin ligase complex [GO:0019005]
Protein-protein interaction112391
Phylogenetic treeP63208
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. CD30.681988787268480.03798388240725080.0792816889131816
AZA vs. DISU0.1508456823253420.5502591127905690.946907720331775
AZA vs. IL70.01119319318906530.9534593420640350.999311006273513
AZA vs. SAHA0.08780463870457250.7191777697618520.921417575584746
DISU vs. CD3-0.5439654426788410.1344774496645920.235300415118289
DISU vs. IL7-0.1486167724577730.5545664758380330.855077183518292
DISU vs. SAHA-0.06203211639036660.831418595521750.956295762245554
DMSO vs. AZA-0.1424604241494880.3939085232062941
DMSO vs. CD3-0.835963801727310.009401083822623390.0236439612333592
DMSO vs. DISU-0.2952158968266820.2257622137064550.738433869372813
DMSO vs. IL70.1608801406303950.3699592714976750.82919060627824
DMSO vs. SAHA0.2232932468826460.343897713987260.695418265120261
HIV vs. Mock in Activation-0.2349668696795430.7054576031206520.999983755607037
HIV vs. Mock in Latency-0.0688778795482120.6756553121740440.999834320637052
IL7 vs. CD3-0.6624055599983140.03981324695046670.091237143549966
SAHA vs. CD3-0.6194389672300430.08249764365009060.149176804632453
SAHA vs. IL70.07300622340512780.7647013398802840.895309359017895
(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 -0.906638275
(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 -0.285426 0.0591778
(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
0.909 1.159 1.055 0.976 1.101
(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
200719_at 1.58 No downregulated in CD8+ cells

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB06980 (2S)-2-(1H-indol-3-yl)hexanoic acid experimental unknown unknown
DB06981 (2S)-2-(1H-indol-3-yl)pentanoic acid experimental unknown unknown
DB06982 (2S)-8-[(tert-butoxycarbonyl)amino]-2-(1H-indol-3-yl)octanoic acid experimental unknown unknown
DB07950 1H-INDOL-3-YLACETIC ACID experimental unknown unknown
DB01750 Naphthalen-1-Yl-Acetic Acid experimental unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1FQV X-ray 2.8Å B/D/F/H/J/L/N/P=1-69# B/D/F/H/J/L/N/P=83-163.
1FS1 X-ray 1.8Å B/D=1-147.
1FS2 X-ray 2.9Å B/D=1-147.
1LDK X-ray 3.1Å D=2-140.
1P22 X-ray 2.9Å B=1-163.
2ASS X-ray 3.0Å A=2-160.
2AST X-ray 2.3Å A=2-160.
2E31 X-ray 2.4Å B=1-163.
2E32 X-ray 3.5Å B/D=1-163.
2OVP X-ray 2.9Å A=1-69# A=82-149.
2OVQ X-ray 2.6Å A=1-69# A=82-149.
2OVR X-ray 2.5Å A=1-69# A=82-149.
3L2O X-ray 2.8Å A=1-69# A=82-163.
3WSO X-ray 2.6Å B=1-163.
4I6J X-ray 2.7Å C=1-163.
5IBK X-ray 2.5Å A/D=1-69# A/D=82-163.
5JH5 X-ray 2.5Å B=2-163.

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

HIV Partner Interaction Type PubMed
Vpu interacts with 22190034

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04110 Cell cycle - Homo sapiens (human)
hsa04114 Oocyte meiosis - Homo sapiens (human)
hsa04120 Ubiquitin mediated proteolysis - Homo sapiens (human)
hsa04141 Protein processing in endoplasmic reticulum - Homo sapiens (human)
hsa04310 Wnt signaling pathway - Homo sapiens (human)
hsa04350 TGF-beta signaling pathway - Homo sapiens (human)
hsa04710 Circadian rhythm - Homo sapiens (human)
hsa05168 Herpes simplex infection - Homo sapiens (human)
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