Q9Z0H3 (SNF5_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

Alternative name(s):
BRG1-associated factor 47
Short name=BAF47
Integrase interactor 1 protein
SNF5 homolog
Short name=mSNF5

Gene names

Name:	Smarcb1
Synonyms:	Baf47, Ini1, Snf5l1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	385 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Core component of the BAF (SWI/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. Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene By similarity. 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 post-mitotic 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 post-mitotic 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. Ref.4
Subunit structure	Component of the BAF (hSWI/SNF) complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57 SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. Interacts with MYK and MAEL. Interacts with PPP1R15A By similarity. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin. Ref.3 Ref.4
Subcellular location	Nucleus.
Developmental stage	Expressed ubiquitously throughout the developing spinal cord, brain and other embryonic tissues at E10.5-E16.5. Ref.4
Sequence similarities	Belongs to the SNF5 family.

Ontologies

Keywords
Biological process	Cell cycle Neurogenesis Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Disease	Tumor suppressor
Domain	Repeat
Molecular function	Activator Chromatin regulator
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ATP-dependent chromatin remodeling Inferred from Biological aspect of Ancestor. Source: RefGenome DNA repair Inferred from Biological aspect of Ancestor. Source: RefGenome blastocyst hatching Inferred from mutant phenotype PubMed 11263494PubMed 11313485. Source: MGI cell differentiation Inferred from mutant phenotype PubMed 16138077. Source: MGI mitotic cell cycle phase transition Inferred from Biological aspect of Ancestor. Source: RefGenome negative regulation of cell proliferation Inferred from mutant phenotype PubMed 11095756PubMed 11263494PubMed 11313485. Source: MGI nervous system development Inferred from electronic annotation. Source: UniProtKB-KW nucleosome disassembly Inferred from Biological aspect of Ancestor. Source: RefGenome positive regulation by host of viral transcription Inferred from electronic annotation. Source: Compara positive regulation of sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: Compara positive regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara regulation of transcription from RNA polymerase II promoter Inferred from Biological aspect of Ancestor. Source: RefGenome retroviral genome replication Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	SWI/SNF complex Inferred from direct assay PubMed 16287714. Source: MGI XY body Inferred from direct assay Ref.3. Source: UniProtKB nBAF complex Inferred from direct assay Ref.4. Source: UniProtKB npBAF complex Inferred from direct assay Ref.4. Source: UniProtKB nuclear chromosome Inferred from electronic annotation. Source: InterPro nucleolus Inferred from electronic annotation. Source: Compara
Molecular_function	transcription coactivator activity Inferred from electronic annotation. Source: Compara
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Smarcc1	P97496	5	EBI-689365,EBI-648047

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform A (identifier: Q9Z0H3-1)

Also known as: INI1A;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform B (identifier: Q9Z0H3-2)

Also known as: INI1B;

The sequence of this isoform differs from the canonical sequence as follows:
     69-77: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 385	385	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1		PRO_0000205949
Regions
	Repeat	186 – 245	60	1
	Repeat	259 – 319	61	2
	Region	106 – 183	78	DNA-binding Potential
	Region	186 – 319	134	2 X approximate tandem repeats
	Region	186 – 245	60	MYC-binding By similarity
	Region	304 – 318	15	Interaction with PPP1R15A By similarity
Amino acid modifications
	Modified residue	129	1	Phosphoserine By similarity
Natural variations
	Alternative sequence	69 – 77	9	Missing in isoform B.		VSP_004400

Sequences

	Sequence		Length	Mass (Da)
	Isoform A (INI1A) [UniParc]. Last modified May 1, 1999. Version 1. Checksum: B7BCA26875BD943D	FASTA	385	44,141
	10 20 30 40 50 60 MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER 70 80 90 100 110 120 KKIVASSHGK KTKPNTKDHG YTTLATSVTL LKASEVEEIL DGNDEKYKAV SISTEPPTYL 130 140 150 160 170 180 REQKAKRNSQ WVPTLPNSSH HLDAVPCSTT INRNRMGRDK KRTFPLCFDD HDPAVIHENA 190 200 210 220 230 240 SQPEVLVPIR LDMEIDGQKL RDAFTWNMNE KLMTPEMFSE ILCDDLDLNP LTFVPAIASA 250 260 270 280 290 300 IRQQIESYPT DSILEDQSDQ RVIIKLNIHV GNISLVDQFE WDMSEKENSP EKFALKLCSE 310 320 330 340 350 360 LGLGGEFVTT IAYSIRGQLS WHQKTYAFSE NPLPTVEIAI RNTGDADQWC PLLETLTDAE 370 380 MEKKIRDQDR NTRRMRRLAN TAPAW
	Isoform B (INI1B) [UniParc]. Checksum: 6C7233EAFBC389A9	FASTA	376	43,158
	10 20 30 40 50 60 MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER 70 80 90 100 110 120 KKIVASSHDH GYTTLATSVT LLKASEVEEI LDGNDEKYKA VSISTEPPTY LREQKAKRNS 130 140 150 160 170 180 QWVPTLPNSS HHLDAVPCST TINRNRMGRD KKRTFPLCFD DHDPAVIHEN ASQPEVLVPI 190 200 210 220 230 240 RLDMEIDGQK LRDAFTWNMN EKLMTPEMFS EILCDDLDLN PLTFVPAIAS AIRQQIESYP 250 260 270 280 290 300 TDSILEDQSD QRVIIKLNIH VGNISLVDQF EWDMSEKENS PEKFALKLCS ELGLGGEFVT 310 320 330 340 350 360 TIAYSIRGQL SWHQKTYAFS ENPLPTVEIA IRNTGDADQW CPLLETLTDA EMEKKIRDQD 370 RNTRRMRRLA NTAPAW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The mouse ortholog of the human SMARCB1 gene encodes two splice forms." Bruder C.E., Dumanski J.P., Kedra D. Biochem. Biophys. Res. Commun. 257:886-890(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B).
[2]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A). Strain: C57BL/6J. Tissue: Tongue.
[3]	"Mouse MAELSTROM: the link between meiotic silencing of unsynapsed chromatin and microRNA pathway?" Costa Y., Speed R.M., Gautier P., Semple C.A., Maratou K., Turner J.M.A., Cooke H.J. Hum. Mol. Genet. 15:2324-2334(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH MAEL.
[4]	"An essential switch in subunit composition of a chromatin remodeling complex during neural development." Lessard J., Wu J.I., Ranish J.A., Wan M., Winslow M.M., Staahl B.T., Wu H., Aebersold R., Graef I.A., Crabtree G.R. Neuron 55:201-215(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE NBAF AND NPBAF COMPLEXES, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE NBAF AND NPBAF COMPLEXES, DEVELOPMENTAL STAGE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ011740 mRNA. Translation: CAA09761.1. AJ011739 mRNA. Translation: CAA09760.1. BC025163 mRNA. Translation: AAH25163.1.
IPI	IPI00129145. IPI00350396.
RefSeq	NP_035548.1. NM_011418.2.
UniGene	Mm.279751. Mm.405473.
3D structure databases
ProteinModelPortal	Q9Z0H3.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-34373N.
IntAct	Q9Z0H3. 8 interactions.
MINT	MINT-4135037.
PTM databases
PhosphoSite	Q9Z0H3.
Proteomic databases
PaxDb	Q9Z0H3.
PRIDE	Q9Z0H3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000000925; ENSMUSP00000000925; ENSMUSG00000000902. ENSMUST00000121304; ENSMUSP00000112463; ENSMUSG00000000902.
GeneID	20587.
KEGG	mmu:20587.
UCSC	uc007ftm.2. mouse.
Organism-specific databases
CTD	6598.
MGI	MGI:1328366. Smarcb1.
Phylogenomic databases
eggNOG	NOG291299.
GeneTree	ENSGT00440000038585.
HOGENOM	HOG000015760.
HOVERGEN	HBG011709.
InParanoid	Q9Z0H3.
KO	K11648.
OMA	QFAEVLC.
OrthoDB	EOG4BK53X.
Gene expression databases
ArrayExpress	Q9Z0H3.
Bgee	Q9Z0H3.
Genevestigator	Q9Z0H3.
GermOnline	ENSMUSG00000000902. Mus musculus.
Family and domain databases
InterPro	IPR006939. SNF5. IPR017393. SWI_SNF_chromatin_remodel_cplx. [Graphical view]
PANTHER	PTHR10019. PTHR10019. 1 hit.
Pfam	PF04855. SNF5. 2 hits. [Graphical view]
PIRSF	PIRSF038126. SWI_SNF. 1 hit.
ProtoNet	Search...
Other
NextBio	298887.
SOURCE	Search...

Entry information

Entry name

SNF5_MOUSE

Accession

Primary (citable) accession number: Q9Z0H3

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 2000
Last sequence update:	May 1, 1999
Last modified:	May 29, 2013
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program