Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0003880
UniProt IDP54252
Primary gene name(s)ATXN3
Synonym gene name(s)ATX3, MJD, MJD1, SCA3
Protein nameAtaxin-3
Protein functionDeubiquitinating enzyme involved in protein homeostasis maintenance, transcription, cytoskeleton regulation, myogenesis and degradation of misfolded chaperone substrates. Binds long polyubiquitin chains and trims them, while it has weak or no activity against chains of 4 or less ubiquitins. Involved in degradation of misfolded chaperone substrates via its interaction with STUB1/CHIP: recruited to monoubiquitinated STUB1/CHIP, and restricts the length of ubiquitin chain attached to STUB1/CHIP substrates and preventing further chain extension. In response to misfolded substrate ubiquitination, mediates deubiquitination of monoubiquitinated STUB1/CHIP. Interacts with key regulators of transcription and represses transcription: acts as a histone-binding protein that regulates transcription. {ECO:0000269|PubMed:12297501, ECO:0000269|PubMed:16118278, ECO:0000269|PubMed:17696782, ECO:0000269|PubMed:23625928}.
Subcellular locationNucleus matrix {ECO:0000269|PubMed:9580663}. Note=Predominantly nuclear, but not exclusively, inner nuclear matrix.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P54252
Gene Ontology
(Biological Process)
Complete annatation
actin cytoskeleton organization [GO:0030036];
cellular response to heat [GO:0034605];
cellular response to misfolded protein [GO:0071218];
chemical synaptic transmission [GO:0007268];
intermediate filament cytoskeleton organization [GO:0045104];
microtubule cytoskeleton organization [GO:0000226];
misfolded or incompletely synthesized protein catabolic process [GO:0006515];
monoubiquitinated protein deubiquitination [GO:0035520];
nervous system development [GO:0007399];
nucleotide-excision repair [GO:0006289];
positive regulation of ERAD pathway [GO:1904294];
proteasome-mediated ubiquitin-dependent protein catabolic process [GO:0043161];
protein deubiquitination [GO:0016579];
protein K48-linked deubiquitination [GO:0071108];
protein K63-linked deubiquitination [GO:0070536];
protein localization to cytosolic proteasome complex involved in ERAD pathway [GO:1904379];
regulation of cell-substrate adhesion [GO:0010810];
regulation of transcription, DNA-templated [GO:0006355];
transcription, DNA-templated [GO:0006351];
ubiquitin-dependent protein catabolic process [GO:0006511]
Gene Ontology
(Molecular Function)
Complete annatation
ATPase binding [GO:0051117];
histone deacetylase activity [GO:0004407];
identical protein binding [GO:0042802];
Lys48-specific deubiquitinase activity [GO:1990380];
Lys63-specific deubiquitinase activity [GO:0061578];
omega peptidase activity [GO:0008242];
RNA polymerase II regulatory region DNA binding [GO:0001012];
thiol-dependent ubiquitin-specific protease activity [GO:0004843];
ubiquitin protein ligase binding [GO:0031625]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytosol [GO:0005829];
mitochondrial matrix [GO:0005759];
mitochondrial membrane [GO:0031966];
nuclear inclusion body [GO:0042405];
nuclear matrix [GO:0016363];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction110433
Phylogenetic treeP54252
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. CD30.4447257331910510.1760634955213580.276362112528421
AZA vs. DISU0.4777152501962020.06314113337228060.554017746098172
AZA vs. IL7-0.1152548760609860.5539753772662950.999311006273513
AZA vs. SAHA-0.485332964374070.05124966710413980.274338594434589
DISU vs. CD30.02067085272369430.9550774884969380.970797206537591
DISU vs. IL7-0.6013400327082570.01862460895794530.170611267381767
DISU vs. SAHA-0.9635233900761040.001095450427326730.02222009877556
DMSO vs. AZA-0.1355349187918490.4266153719580681
DMSO vs. CD3-0.5883929845456210.06719205596372760.123234837280473
DMSO vs. DISU-0.6138676662257340.01348302027140350.24295084121958
DMSO vs. IL70.02676725158074890.883322022062390.974984430449502
DMSO vs. SAHA-0.3587199818356040.1357839281716090.441739770212697
HIV vs. Mock in Activation-0.04952949461704990.936611689321140.999983755607037
HIV vs. Mock in Latency0.1854917804440840.2685005677627290.999834320637052
IL7 vs. CD3-0.5507874322598790.08826085576771280.172013948666503
SAHA vs. CD3-0.9564839748211520.008052027492678640.0213935215646451
SAHA vs. IL7-0.3755846246979840.1290895123682350.334748892041763
(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) unknown
(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 -0.0949327 0.832416
(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
0.999 0.914 0.881 0.906 1.017
(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
205416_s_at 1.63 No upregulated in CD8+ cells

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
1YZB NMR - A=1-182.
2AGA NMR - A=1-185.
2DOS NMR - A=1-171.
2JRI NMR - A=1-182.
2KLZ NMR - A=222-263.
4WTH X-ray 2.2Å A/B=278-324.
4YS9 X-ray 2.0Å B=278-324.

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04141 Protein processing in endoplasmic reticulum - Homo sapiens (human)