Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002530
UniProt IDP27694
Primary gene name(s)RPA1
Synonym gene name(s)REPA1, RPA70
Protein nameReplication protein A 70 kDa DNA-binding subunit
Protein functionAs part of the heterotrimeric replication protein A complex, RPA/RP-A, binds and stabilizes single-stranded DNA intermediates, that form during DNA replication or upon DNA stress. It prevents their reannealing and in parallel, recruits and activates different proteins and complexes involved in DNA metabolism, PubMed:27723720, PubMed:27723717. Thereby, it plays an essential role both in DNA replication and the cellular response to DNA damage, PubMed:9430682. In the cellular response to DNA damage, the RPA complex controls DNA repair and DNA damage checkpoint activation. Through recruitment of ATRIP activates the ATR kinase a master regulator of the DNA damage response, PubMed:24332808. It is required for the recruitment of the DNA double-strand break repair factors RAD51 and RAD52 to chromatin in response to DNA damage, PubMed:17765923. Also recruits to sites of DNA damage proteins like XPA and XPG that are involved in nucleotide excision repair and is required for this mechanism of DNA repair, PubMed:7697716. Plays also a role in base excision repair, BER probably through interaction with UNG, PubMed:9765279. Through RFWD3 may activate CHEK1 and play a role in replication checkpoint control. Also recruits SMARCAL1/HARP, which is involved in replication fork restart, to sites of DNA damage. May also play a role in telomere maintenance, PubMed:17959650. As part of the alternative replication protein A complex, aRPA, binds single-stranded DNA and probably plays a role in DNA repair. Compared to the RPA2-containing, canonical RPA complex, may not support chromosomal DNA replication and cell cycle progression through S-phase. The aRPA may not promote efficient priming by DNA polymerase alpha but could support DNA synthesis by polymerase delta in presence of PCNA and replication factor C, RFC, the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange, PubMed:19996105. {ECO:0000269|PubMed:12791985, ECO:0000269|PubMed:17765923, ECO:0000269|PubMed:17959650, ECO:0000269|PubMed:19116208, ECO:0000269|PubMed:19996105, ECO:0000269|PubMed:24332808, ECO:0000269|PubMed:27723717, ECO:0000269|PubMed:27723720, ECO:0000269|PubMed:7697716, ECO:0000269|PubMed:7700386, ECO:0000269|PubMed:9430682, ECO:0000269|PubMed:9765279}.
Subcellular locationNucleus {ECO:0000269|PubMed:17959650}. Nucleus, PML body {ECO:0000269|PubMed:17959650}. Note=Enriched in PML bodies in cells displaying alternative lengthening of their telomeres. {ECO:0000269|PubMed:17959650}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P27694
Gene Ontology
(Biological Process)
Complete annatation
base-excision repair [GO:0006284];
DNA damage response, detection of DNA damage [GO:0042769];
DNA-dependent DNA replication [GO:0006261];
DNA recombination [GO:0006310];
DNA repair [GO:0006281];
DNA replication [GO:0006260];
double-strand break repair via homologous recombination [GO:0000724];
error-free translesion synthesis [GO:0070987];
error-prone translesion synthesis [GO:0042276];
G1/S transition of mitotic cell cycle [GO:0000082];
interstrand cross-link repair [GO:0036297];
mismatch repair [GO:0006298];
nucleotide-excision repair [GO:0006289];
nucleotide-excision repair, DNA gap filling [GO:0006297];
nucleotide-excision repair, DNA incision [GO:0033683];
nucleotide-excision repair, DNA incision, 3'-to lesion [GO:0006295];
nucleotide-excision repair, DNA incision, 5'-to lesion [GO:0006296];
nucleotide-excision repair, preincision complex assembly [GO:0006294];
nucleotide-excision repair, preincision complex stabilization [GO:0006293];
protein sumoylation [GO:0016925];
regulation of cellular response to heat [GO:1900034];
regulation of signal transduction by p53 class mediator [GO:1901796];
telomere maintenance [GO:0000723];
telomere maintenance via recombination [GO:0000722];
transcription-coupled nucleotide-excision repair [GO:0006283];
translesion synthesis [GO:0019985]
Gene Ontology
(Molecular Function)
Complete annatation
damaged DNA binding [GO:0003684];
metal ion binding [GO:0046872];
single-stranded DNA binding [GO:0003697]
Gene Ontology
(Cellular Component)
Complete annatation
DNA replication factor A complex [GO:0005662];
nuclear chromosome, telomeric region [GO:0000784];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
PML body [GO:0016605]
Protein-protein interaction112037
Phylogenetic treeP27694
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. CD30.6634300136974250.0452923305032480.0920444083920006
AZA vs. DISU0.01877827314510380.9407204814812410.996198528027442
AZA vs. IL70.07489313914220760.6964617952356860.999311006273513
AZA vs. SAHA0.09863779441479060.6864765852028840.909717060895527
DISU vs. CD3-0.6566202046787780.07393839033287260.147057302530376
DISU vs. IL70.04634339985501580.8539798579165150.970892912436268
DISU vs. SAHA0.08194893285023420.7786554407601770.938812478052457
DMSO vs. AZA0.02051747284694480.9022929798209541
DMSO vs. CD3-0.6529818532589730.04316850126214420.0849998002240495
DMSO vs. DISU0.0002159332943597220.9992929398484260.999828688118659
DMSO vs. IL70.06140204685610550.7322269315928640.946333083680773
DMSO vs. SAHA0.07200450815098780.7607609923098390.93064423709115
HIV vs. Mock in Activation0.1535989134674750.8047916507219550.999983755607037
HIV vs. Mock in Latency0.05620133504799180.7908084868276170.999834320637052
IL7 vs. CD3-0.582425873645280.07150025075706820.145993400116674
SAHA vs. CD3-0.5885539336351140.1045991351236530.180396997747018
SAHA vs. IL70.02132484893427930.9306482137739420.974140071830317
(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 0.43014 0.00221059
(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
1.049 1.02 1.049 1.038 1.036
(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
1EWI NMR - A=1-114.
1FGU X-ray 2.5Å A/B=182-432.
1JMC X-ray 2.4Å A=181-422.
1L1O X-ray 2.8Å C/F=436-616.
2B29 X-ray 1.6Å A=1-120.
2B3G X-ray 1.6Å A=1-120.
4IJH X-ray 1.5Å A=1-120.
4IJL X-ray 1.7Å A=1-120.
4IPC X-ray 1.2Å A=1-120.
4IPD X-ray 1.5Å A=1-120.
4IPG X-ray 1.5Å A=1-120.
4IPH X-ray 1.9Å A=1-120.
4LUO X-ray 1.5Å A=1-120.
4LUV X-ray 1.4Å A=1-120.
4LUZ X-ray 1.9Å A=1-120.
4LW1 X-ray 1.6Å A=1-120.
4LWC X-ray 1.6Å A=1-120.
4NB3 X-ray 1.3Å A/B=1-120.
4O0A X-ray 1.2Å A=1-120.
4R4C X-ray 1.4Å A=1-120.
4R4I X-ray 1.4Å A=1-120.
4R4O X-ray 1.3Å A=1-120.
4R4Q X-ray 1.3Å A=1-120.
4R4T X-ray 1.2Å A=1-120.
5E7N X-ray 1.2Å A=1-120.
5EAY X-ray 1.5Å A/B/C/D=3-120.

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

HIV Partner Interaction Type PubMed
Vpr interacts with 16306615
19275579
24158819
reverse transcriptase inhibited by 9084803
Tat interacts with 9121429

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03030 DNA replication - Homo sapiens (human)
hsa03420 Nucleotide excision repair - Homo sapiens (human)
hsa03430 Mismatch repair - Homo sapiens (human)
hsa03440 Homologous recombination - Homo sapiens (human)
hsa03460 Fanconi anemia pathway - Homo sapiens (human)
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