Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002073
UniProt IDP11940
Primary gene name(s)PABPC1
Synonym gene name(s)PAB1, PABP1, PABPC2
Protein namePolyadenylate-binding protein 1
Protein functionBinds the poly(A tail of mRNA, including that of its own transcript. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability, mCRD domain. Involved in regulation of nonsense-mediated decay, NMD of mRNAs containing premature stop codons; for the recognition of premature termination codons, PTC and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. By binding to long poly(A tails, may protect them from uridylation by ZCCHC6/ZCCHC11 and hence contribute to mRNA stability, PubMed:25480299. Positively regulates the replication of dengue virus, DENV, PubMed:26735137. {ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:17212783, ECO:0000269|PubMed:18447585, ECO:0000269|PubMed:20573744, ECO:0000269|PubMed:25480299, ECO:0000269|PubMed:26735137}.
Subcellular locationCytoplasm. Nucleus. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Shuttles between the cytoplasm and the nucleus.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P11940
Gene Ontology
(Biological Process)
Complete annatation
gene silencing by RNA [GO:0031047];
mRNA polyadenylation [GO:0006378];
mRNA splicing, via spliceosome [GO:0000398];
mRNA stabilization [GO:0048255];
negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:2000623];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
nuclear-transcribed mRNA poly(A tail shortening [GO:0000289];
positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay [GO:1900153];
positive regulation of nuclear-transcribed mRNA poly(A tail shortening [GO:0060213];
positive regulation of viral genome replication [GO:0045070];
regulation of mRNA stability [GO:0043488];
translational initiation [GO:0006413]
Gene Ontology
(Molecular Function)
Complete annatation
nucleotide binding [GO:0000166];
poly(A binding [GO:0008143];
poly(A RNA binding [GO:0044822];
poly(U RNA binding [GO:0008266];
protein C-terminus binding [GO:0008022];
translation activator activity [GO:0008494]
Gene Ontology
(Cellular Component)
Complete annatation
catalytic step 2 spliceosome [GO:0071013];
cytoplasm [GO:0005737];
cytoplasmic ribonucleoprotein granule [GO:0036464];
cytoplasmic stress granule [GO:0010494];
cytosol [GO:0005829];
extracellular exosome [GO:0070062];
focal adhesion [GO:0005925];
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
nucleus [GO:0005634]
Protein-protein interaction117939
Phylogenetic treeP11940
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. CD30.3023912211690690.3572132727427580.478655622935531
AZA vs. DISU-0.2035628083507380.4201316570417510.911342924190573
AZA vs. IL7-0.005349706741493740.9777537637031730.999311006273513
AZA vs. SAHA0.02407104135698330.9212510772367650.982071981797342
DISU vs. CD3-0.5173822609291890.1577067000465140.265913959340174
DISU vs. IL70.189248403285680.4514382861285160.797079038530056
DISU vs. SAHA0.2279194800775710.4353268272646510.781929674836169
DMSO vs. AZA-0.1732201951852380.2984764013403431
DMSO vs. CD3-0.4874523152170590.1295415703863210.210727109153431
DMSO vs. DISU0.0282365841459160.9076339134621790.988283279918411
DMSO vs. IL70.1751974941231770.328605225667150.80304552824776
DMSO vs. SAHA0.1896178166497440.4208449594899090.760230028234601
HIV vs. Mock in Activation-0.1379805122969360.8242104777862050.999983755607037
HIV vs. Mock in Latency-0.05753053711923340.7258539862321830.999834320637052
IL7 vs. CD3-0.2988675579057360.3584762204286310.495762186486903
SAHA vs. CD3-0.3047721309522780.3879652856539530.504542358888943
SAHA vs. IL70.02490560461265410.9189554317009490.969304749664831
(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 0.552705 0.403837
(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
0.963 0.951 0.788 0.776 0.952
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
0.5 0.0007 -0.03 0.1593 -0.3 0.0022 Protein Synthesis at 4; 8; and 20 hip
(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
1CVJ X-ray 2.6Å A/B/C/D/E/F/G/H=1-190.
1G9L NMR - A=498-636.
1JGN NMR - A=544-636.
1JH4 NMR - A=544-636.
2K8G NMR - A=90-182.
2RQG NMR - B=541-623.
2RQH NMR - B=541-623.
2X04 X-ray 1.4Å A/B=545-619.
3KTP X-ray 1.5Å A=544-626.
3KTR X-ray 1.7Å A=544-626.
3KUI X-ray 2.3Å A=544-626.
3KUJ X-ray 1.4Å A=544-626.
3KUR X-ray 2.5Å A/B/C/D/E/F/G/H=544-617.
3KUS X-ray 1.4Å A/B=544-626.
3KUT X-ray 1.5Å A/B=544-626.
3PKN X-ray 1.8Å A=544-626.
3PTH X-ray 1.7Å A=543-621.
4F02 X-ray 2.0Å A/D=1-190.
4F25 X-ray 1.9Å A=99-199.
4F26 X-ray 2.0Å A=99-199.
5DX1 X-ray 1.9Å F/G/H/I=449-466.
5DX8 X-ray 1.9Å E/F/G/H=449-466.
5DXA X-ray 2.0Å F/G/I=449-466.

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

HIV Partner Interaction Type PubMed
Rev interacts with 22174317
Envelope surface glycoprotein gp120 complexes with 23125841
retropepsin cleaves 16594896
Gag-Pol complexes with 23125841
Pr55(Gag) complexes with 23125841
Tat interacts with 25496916
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03013 RNA transport - Homo sapiens (human)
hsa03015 mRNA surveillance pathway - Homo sapiens (human)
hsa03018 RNA degradation - Homo sapiens (human)