Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002768
UniProt IDQ12824
Primary gene name(s)SMARCB1
Synonym gene name(s)BAF47, INI1, SNF5L1
Protein nameSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Protein functionCore component of the BAF, hSWI/SNF complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex, npBAF complex and the neuron-specific chromatin remodeling complex, nBAF complex. During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes, nBAF. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth, By similarity. Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1. {ECO:0000250, ECO:0000269|PubMed:10078207, ECO:0000269|PubMed:12226744, ECO:0000269|PubMed:14604992, ECO:0000269|PubMed:16267391, ECO:0000269|PubMed:16314535, ECO:0000269|PubMed:9448295}.
Subcellular locationNucleus.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q12824
Gene Ontology
(Biological Process)
Complete annatation
ATP-dependent chromatin remodeling [GO:0043044];
blastocyst hatching [GO:0001835];
cell cycle [GO:0007049];
cell differentiation [GO:0030154];
chromatin remodeling [GO:0006338];
covalent chromatin modification [GO:0016569];
DNA integration [GO:0015074];
DNA repair [GO:0006281];
negative regulation of cell proliferation [GO:0008285];
negative regulation of histone H3-K9 dimethylation [GO:1900110];
negative regulation of histone H3-K9 trimethylation [GO:1900113];
nervous system development [GO:0007399];
nucleosome disassembly [GO:0006337];
positive regulation by host of viral transcription [GO:0043923];
positive regulation of glucose mediated signaling pathway [GO:1902661];
positive regulation of histone H3-K9 acetylation [GO:2000617];
positive regulation of histone H4 acetylation [GO:0090240];
positive regulation of sequence-specific DNA binding transcription factor activity [GO:0051091];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter [GO:1901838];
regulation of transcription from RNA polymerase II promoter [GO:0006357];
single stranded viral RNA replication via double stranded DNA intermediate [GO:0039692];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
p53 binding [GO:0002039];
RNA polymerase I CORE element sequence-specific DNA binding [GO:0001164];
Tat protein binding [GO:0030957];
transcription coactivator activity [GO:0003713]
Gene Ontology
(Cellular Component)
Complete annatation
nBAF complex [GO:0071565];
npBAF complex [GO:0071564];
nuclear chromatin [GO:0000790];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
protein complex [GO:0043234];
SWI/SNF complex [GO:0016514];
XY body [GO:0001741]
Protein-protein interaction112482
Phylogenetic treeQ12824
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. CD30.7350681092940540.02557756304831960.0570273713408688
AZA vs. DISU0.1074592523412330.6722464143194280.964163205732993
AZA vs. IL70.2147732199327030.2669315171178440.999311006273513
AZA vs. SAHA-1.261286956004310.002547631815679850.0395092613061297
DISU vs. CD3-0.6392662526709030.07895135370166980.154720840574489
DISU vs. IL70.09774844858251440.6983658182732050.922646480565402
DISU vs. SAHA-1.366777604742590.00147567068906540.0270362073313144
DMSO vs. AZA-0.06128572737766990.7164788486882441
DMSO vs. CD3-0.807572042281970.01208585154175710.0292957929970348
DMSO vs. DISU-0.1705611204598880.486212452724380.903702721084904
DMSO vs. IL70.283332489171250.1174591791374420.607956301966704
DMSO vs. SAHA-1.205491244355480.003527923116116830.0432270969780461
HIV vs. Mock in Activation0.1571519199359350.8008345546140310.999983755607037
HIV vs. Mock in Latency-0.03478157177782150.8553560483332230.999834320637052
IL7 vs. CD3-0.5141479591109520.1104184488309520.20462164999694
SAHA vs. CD3-2.019444549649171.35097614617496e-061.0614812577089e-05
SAHA vs. IL7-1.478273286541590.0003048335006419210.00470172166773338
(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 -1.263135509
(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 0.161504 0.334774
(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
1.023 1.098 1.049 1.053 1.117
(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
5AJ1 NMR - A=2-113.

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

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found