Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000764
UniProt IDQ16531
Primary gene name(s)DDB1
Synonym gene name(s)XAP1
Protein nameDNA damage-binding protein 1
Protein functionRequired for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex, the UV-DDB complex. The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway, the NER pathway to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers, CPD, 6-4 photoproducts, 6-4 PP, apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX, DDB1-CUL4-X-box E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2, also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1 may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2 also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8, the CSA complex plays a role in transcription-coupled repair, TCR. May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2. {ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:14739464, ECO:0000269|PubMed:15448697, ECO:0000269|PubMed:15882621, ECO:0000269|PubMed:16260596, ECO:0000269|PubMed:16407242, ECO:0000269|PubMed:16407252, ECO:0000269|PubMed:16473935, ECO:0000269|PubMed:16482215, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:16940174, ECO:0000269|PubMed:17041588, ECO:0000269|PubMed:17079684, ECO:0000269|PubMed:18332868, ECO:0000269|PubMed:18381890, ECO:0000269|PubMed:18593899, ECO:0000269|PubMed:19966799, ECO:0000269|PubMed:22118460, ECO:0000269|PubMed:25043012, ECO:0000269|PubMed:25108355}.
Subcellular locationCytoplasm. Nucleus. Note=Primarily cytoplasmic. Translocates to the nucleus following UV irradiation and subsequently accumulates at sites of DNA damage.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q16531
Gene Ontology
(Biological Process)
Complete annatation
DNA damage response, detection of DNA damage [GO:0042769];
DNA repair [GO:0006281];
global genome nucleotide-excision repair [GO:0070911];
histone H2A monoubiquitination [GO:0035518];
interaction with symbiont [GO:0051702];
negative regulation of apoptotic process [GO:0043066];
nucleotide-excision repair [GO:0006289];
nucleotide-excision repair, DNA damage recognition [GO:0000715];
nucleotide-excision repair, DNA duplex unwinding [GO:0000717];
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];
positive regulation by virus of viral protein levels in host cell [GO:0046726];
positive regulation of viral genome replication [GO:0045070];
positive regulation of viral release from host cell [GO:1902188];
proteasome-mediated ubiquitin-dependent protein catabolic process [GO:0043161];
protein ubiquitination involved in ubiquitin-dependent protein catabolic process [GO:0042787];
regulation of mitotic cell cycle phase transition [GO:1901990];
transcription-coupled nucleotide-excision repair [GO:0006283];
UV-damage excision repair [GO:0070914];
viral process [GO:0016032];
Wnt signaling pathway [GO:0016055]
Gene Ontology
(Molecular Function)
Complete annatation
damaged DNA binding [GO:0003684];
DNA binding [GO:0003677]
Gene Ontology
(Cellular Component)
Complete annatation
Cul4A-RING E3 ubiquitin ligase complex [GO:0031464];
Cul4B-RING E3 ubiquitin ligase complex [GO:0031465];
Cul4-RING E3 ubiquitin ligase complex [GO:0080008];
cytoplasm [GO:0005737];
extracellular exosome [GO:0070062];
extracellular space [GO:0005615];
nuclear chromosome, telomeric region [GO:0000784];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction108009
Phylogenetic treeQ16531
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. CD30.8270983330260790.01215216890732370.0308086610212251
AZA vs. DISU0.03372803620697760.8936919273998660.993789282048992
AZA vs. IL70.2295454695761720.231411459761630.990920320206469
AZA vs. SAHA-0.03727596765001190.8782964777767710.972987514221139
DISU vs. CD3-0.8057008002675190.02737819842858490.0664785700889963
DISU vs. IL70.186550361769230.4581409198339040.800667218287658
DISU vs. SAHA-0.06906152377367050.8123337301485820.951385325391594
DMSO vs. AZA0.06252989762900090.708020758451441
DMSO vs. CD3-0.7764282458256870.0160029817760190.0370785789688905
DMSO vs. DISU0.02676806711871360.9124464401118150.988283279918411
DMSO vs. IL70.1744367202274790.330587634133650.804163215195171
DMSO vs. SAHA-0.1057124895317060.6533521254903260.889342292697539
HIV vs. Mock in Activation0.1325601525798460.831092469315150.999983755607037
HIV vs. Mock in Latency0.006465661131661160.9686601478151310.999834320637052
IL7 vs. CD3-0.5907591376410550.06759305360708020.139699725355755
SAHA vs. CD3-0.8881766482562260.01255111036082320.0310481341328966
SAHA vs. IL7-0.269581176093530.2679242176976770.514745049397755
(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 -0.0280446 0.932167
(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 0.987 0.927 0.85 0.954
(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
2B5L X-ray 2.8Å A/B=1-1140.
2B5M X-ray 2.9Å A=1-1140.
2B5N X-ray 2.8Å A/B/C/D=391-709.
2HYE X-ray 3.1Å A=1-1140.
3E0C X-ray 2.4Å A=1-1140.
3EI1 X-ray 2.8Å A=1-1140.
3EI2 X-ray 2.6Å A=1-1140.
3EI3 X-ray 2.3Å A=1-1140.
3EI4 X-ray 3.3Å A/C/E=1-1140.
3I7H X-ray 2.9Å A=1-1140.
3I7K X-ray 2.8Å A=1-1140.
3I7L X-ray 2.8Å A=1-1140.
3I7N X-ray 2.8Å A=1-1140.
3I7O X-ray 2.8Å A=1-1140.
3I7P X-ray 3.0Å A=1-1140.
3I89 X-ray 3.0Å A=1-1140.
3I8C X-ray 2.8Å A=1-1140.
3I8E X-ray 3.4Å A/B=1-1140.
4A08 X-ray 3.0Å A=1-1140.
4A09 X-ray 3.1Å A=1-1140.
4A0A X-ray 3.6Å A=1-1140.
4A0B X-ray 3.8Å A/C=1-1140.
4A0K X-ray 5.9Å C=1-1140.
4A0L X-ray 7.4Å A/C=1-1140.
4A11 X-ray 3.3Å A=1-1140.
4CI1 X-ray 2.9Å A=1-1140.
4CI2 X-ray 2.9Å A=1-1140.
4CI3 X-ray 3.5Å A=1-1140.
4E54 X-ray 2.8Å A=2-1140.
4E5Z X-ray 3.2Å A=2-1140.
4TZ4 X-ray 3.0Å A=2-1140.
5FQD X-ray 2.4Å A/D=1-395# A/D=709-1140.
5HXB X-ray 3.6Å B/Y=1-1140.
5JK7 X-ray 3.4Å A/B=1-1140.

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

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03420 Nucleotide excision repair - Homo sapiens (human)
hsa04120 Ubiquitin mediated proteolysis - Homo sapiens (human)
hsa05161 Hepatitis B - Homo sapiens (human)
hsa05203 Viral carcinogenesis - Homo sapiens (human)