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Reviewed, UniProtKB/Swiss-Prot Q12824 (SNF5_HUMAN)

Last modified February 9, 2010. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Alternative name(s):
    Integrase interactor 1 protein
      Short name=hSNF5
    BRG1-associated factor 47
      Short name=BAF47
Gene names
Name: SMARCB1
Synonyms: BAF47, INI1, SNF5L1
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length385 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level.

General annotation (Comments)

Function

Core 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 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 By similarity. 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. Ref.9 Ref.13 Ref.16 Ref.17 Ref.18 Ref.19 Ref.21

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. Binds to double-stranded DNA. Interacts with MYK and MAEL. Interacts with PPP1R15A. Binds tightly to the human immunodeficiency virus-type 1 (HIV-1) integrase in vitro and stimulates its DNA-joining activity. Interacts with human papillomavirus 18 E1 protein to stimulates its viral replication. Interacts with Epstein-Barr virus protein EBNA-2. 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 By similarity. Ref.8 Ref.10 Ref.11 Ref.12 Ref.15

Subcellular location

Nucleus.

Post-translational modification

Phosphorylated upon DNA damage, probably by ATM or ATR. Ref.22

Involvement in disease

Defects in SMARCB1 are a cause of rhabdoid tumor (RDT) [MIM:609322]; also known as malignant rhabdoid tumor (MRT). RDT are a highly malignant group of neoplasms that usually occur in early childhood. SMARCB1/INI1 is also frequently inactivated in epithelioid sarcomas. Ref.3 Ref.14 Ref.20

Defects in SMARCB1 are a cause of schwannomatosis [MIM:162091]; also called congenital cutaneous neurilemmomatosis. Schwannomas are benign tumors of the peripheral nerve sheath that usually occur singly in otherwise normal individuals. Multiple schwannomas in the same individual suggest an underlying tumor-predisposition syndrome. The most common such syndrome is NF2. The hallmark of NF2 is the development of bilateral vestibular-nerve schwannomas; but two-thirds or more of all NF2-affected individuals develop schwannomas in other locations, and dermal schwannomas may precede vestibular tumors in NF2-affected children. There have been several reports of individuals with multiple schwannomas who do not show evidence of vestibular schwannoma. Clinical report suggests that schwannomatosis is a clinical entity distinct from other forms of neurofibromatosis. Ref.14 Ref.20 Ref.25 Ref.26

Sequence similarities

Belongs to the SNF5 family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

ARID2Q68CP91EBI-358419,EBI-637818

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform A (identifier: Q12824-1)

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: Q12824-2)

Also known as: INI1B;

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 385385SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
PRO_0000205948

Regions

Repeat186 – 245601
Repeat259 – 319612
Region106 – 18378DNA-binding Potential
Region183 – 24361HIV-1 integrase-binding
Region186 – 3191342 X approximate tandem repeats
Region186 – 24560MYC-binding
Region304 – 31815Interaction with PPP1R15A

Amino acid modifications

Modified residue1291Phosphoserine Ref.22

Natural variations

Alternative sequence69 – 779Missing in isoform B.
VSP_004399

Experimental info

Sequence conflict1361P → S Ref.1
Sequence conflict1361P → S Ref.3
Sequence conflict3781L → E in CAA76639. Ref.3
Sequence conflict3821A → G Ref.1
Sequence conflict3821A → G Ref.3

Sequences

Sequence LengthMass (Da)Tools
Isoform A (INI1A) [UniParc].

Last modified August 16, 2004. Version 2.
Checksum: B7BCA26875BD943D

FASTA38544,141
        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 

« Hide

Isoform B (INI1B).

Checksum: 6C7233EAFBC389A9
Show »

FASTA37643,158

References

« Hide 'large scale' references
[1]"Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5."
Kalpana G.V., Marmon S., Wang W., Crabtree G.R., Goff S.P.
Science 266:2002-2006(1994) [PubMed: 7801128] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A).
[2]"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: 10208879] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B).
[3]"Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer."
Versteege I., Sevenet N., Lange J., Rousseau-Merck M.-F., Ambros P., Handgretinger R., Aurias A., Delattre O.
Nature 394:203-206(1998) [PubMed: 9671307] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INVOLVEMENT IN RDT.
[4]"Human Ini1 27bp deletion form."
Tozaki H., Yasuda J., Iwakura Y.
Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM B).
[5]"A genome annotation-driven approach to cloning the human ORFeome."
Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I.
Genome Biol. 5:R84.1-R84.11(2004) [PubMed: 15461802] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
[6]NIEHS SNPs program
Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[7]"Purification and biochemical heterogeneity of the mammalian SWI-SNF complex."
Wang W., Cote J., Xue Y., Zhou S., Khavari P.A., Biggar S.R., Muchardt C., Kalpana G.V., Goff S.P., Yaniv M., Workman J.L., Crabtree G.R.
EMBO J. 15:5370-5382(1996) [PubMed: 8895581] [Abstract]
Cited for: IDENTIFICATION IN BAF COMPLEX.
[8]"Epstein-Barr virus nuclear protein 2 (EBNA2) binds to a component of the human SNF-SWI complex, hSNF5/Ini1."
Wu D.Y., Kalpana G.V., Goff S.P., Schubach W.H.
J. Virol. 70:6020-6028(1996) [PubMed: 8709224] [Abstract]
Cited for: INTERACTION WITH EPSTEIN-BARR VIRUS EBNA2.
[9]"Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region."
Morozov A., Yung E., Kalpana G.V.
Proc. Natl. Acad. Sci. U.S.A. 95:1120-1125(1998) [PubMed: 9448295] [Abstract]
Cited for: FUNCTION.
[10]"Leukemic HRX fusion proteins inhibit GADD34-induced apoptosis and associate with the GADD34 and hSNF5/INI1 proteins."
Adler H.T., Chinery R., Wu D.Y., Kussick S.J., Payne J.M., Fornace A.J. Jr., Tkachuk D.C.
Mol. Cell. Biol. 19:7050-7060(1999) [PubMed: 10490642] [Abstract]
Cited for: INTERACTION WITH PPP1R15A.
[11]"c-MYC interacts with INI1/hSNF5 and requires the SWI/SNF complex for transactivation function."
Cheng S.-W., Davies K.P., Yung E., Beltran R.J., Yu J., Kalpana G.V.
Nat. Genet. 22:102-105(1999) [PubMed: 10319872] [Abstract]
Cited for: INTERACTION WITH MYC.
[12]"Interaction of E1 and hSNF5 proteins stimulates replication of human papillomavirus DNA."
Lee D., Sohn H., Kalpana G.V., Choe J.
Nature 399:487-491(1999) [PubMed: 10365963] [Abstract]
Cited for: INTERACTION WITH HUMAN PAPILLOMAVIRUS-18 E1 PROTEIN.
[13]"Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits."
Phelan M.L., Sif S., Narlikar G.J., Kingston R.E.
Mol. Cell 3:247-253(1999) [PubMed: 10078207] [Abstract]
Cited for: FUNCTION.
[14]"Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors."
Biegel J.A., Zhou J.-Y., Rorke L.B., Stenstrom C., Wainwright L.M., Fogelgren B.
Cancer Res. 59:74-79(1999) [PubMed: 9892189] [Abstract]
Cited for: DISEASE.
[15]"The human SNF5/INI1 protein facilitates the function of the growth arrest and DNA damage-inducible protein (GADD34) and modulates GADD34-bound protein phosphatase-1 activity."
Wu D.Y., Tkachuck D.C., Roberson R.S., Schubach W.H.
J. Biol. Chem. 277:27706-27715(2002) [PubMed: 12016208] [Abstract]
Cited for: INTERACTION WITH PPP1R15A.
[16]"A key role of the hSNF5/INI1 tumour suppressor in the control of the G1-S transition of the cell cycle."
Versteege I., Medjkane S., Rouillard D., Delattre O.
Oncogene 21:6403-6412(2002) [PubMed: 12226744] [Abstract]
Cited for: FUNCTION IN CELL CYCLE.
[17]"The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome."
Kitagawa H., Fujiki R., Yoshimura K., Mezaki Y., Uematsu Y., Matsui D., Ogawa S., Unno K., Okubo M., Tokita A., Nakagawa T., Ito T., Ishimi Y., Nagasawa H., Matsumoto T., Yanagisawa J., Kato S.
Cell 113:905-917(2003) [PubMed: 12837248] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE WINAC COMPLEX, FUNCTION.
[18]"P16INK4a is required for hSNF5 chromatin remodeler-induced cellular senescence in malignant rhabdoid tumor cells."
Oruetxebarria I., Venturini F., Kekarainen T., Houweling A., Zuijderduijn L.M.P., Mohd-Sarip A., Vries R.G.J., Hoeben R.C., Verrijzer C.P.
J. Biol. Chem. 279:3807-3816(2004) [PubMed: 14604992] [Abstract]
Cited for: FUNCTION IN CELL CYCLE.
[19]"Chromatin-remodeling factor INI1/hSNF5/BAF47 is involved in activation of the colony stimulating factor 1 promoter."
Pan X., Song Z., Zhai L., Li X., Zeng X.
Mol. Cells 20:183-188(2005) [PubMed: 16267391] [Abstract]
Cited for: FUNCTION IN ACTIVATION OF COLONY STIMULATING FACTOR 1 PROMOTER.
[20]"SMARCB1/INI1 tumor suppressor gene is frequently inactivated in epithelioid sarcomas."
Modena P., Lualdi E., Facchinetti F., Galli L., Teixeira M.R., Pilotti S., Sozzi G.
Cancer Res. 65:4012-4019(2005) [PubMed: 15899790] [Abstract]
Cited for: DISEASE.
[21]"Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates."
Ulyanova N.P., Schnitzler G.R.
Mol. Cell. Biol. 25:11156-11170(2005) [PubMed: 16314535] [Abstract]
Cited for: FUNCTION OF BAF COMPLEX IN CHROMATIN REMODELING.
[22]"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage."
Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J.
Science 316:1160-1166(2007) [PubMed: 17525332] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-129, MASS SPECTROMETRY.
[23]"Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex."
Lange M., Kaynak B., Forster U.B., Toenjes M., Fischer J.J., Grimm C., Schlesinger J., Just S., Dunkel I., Krueger T., Mebus S., Lehrach H., Lurz R., Gobom J., Rottbauer W., Abdelilah-Seyfried S., Sperling S.
Genes Dev. 22:2370-2384(2008) [PubMed: 18765789] [Abstract]
Cited for: IDENTIFICATION IN THE BAF COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
[24]Colinge J., Superti-Furga G., Bennett K.L.
Submitted (OCT-2008) to UniProtKB
Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[25]"Germline mutation of INI1/SMARCB1 in familial schwannomatosis."
Hulsebos T.J.M., Plomp A.S., Wolterman R.A., Robanus-Maandag E.C., Baas F., Wesseling P.
Am. J. Hum. Genet. 80:805-810(2007) [PubMed: 17357086] [Abstract]
Cited for: INVOLVEMENT IN SCHWANNOMATOSIS.
[26]"Evidence of a four-hit mechanism involving SMARCB1 and NF2 in schwannomatosis-associated schwannomas."
Sestini R., Bacci C., Provenzano A., Genuardi M., Papi L.
Hum. Mutat. 29:227-231(2008) [PubMed: 18072270] [Abstract]
Cited for: INVOLVEMENT IN SCHWANNOMATOSIS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U04847 mRNA. Translation: AAA81905.1.
AJ011738 mRNA. Translation: CAA09759.1.
AJ011737 mRNA. Translation: CAA09758.1.
Y17118 expand/collapse EMBL AC list , Y17119, Y17120, Y17121, Y17122, Y17123, Y17124, Y17125, Y17126 Genomic DNA. Translation: CAA76639.1. Sequence problems.
AB017523 mRNA. Translation: BAC77068.1.
CR456581 mRNA. Translation: CAG30467.1.
DQ230988 Genomic DNA. Translation: ABB02184.1.
IPIIPI00029695.
IPI00745019.
PIRS54705.
RefSeqNP_001007469.1.
NP_003064.2.
UniGeneHs.534350

3D structure databases

ModBaseSearch...

Protein-protein interaction databases

DIPDIP-27550N.
IntActQ12824. 8 interactions.
STRINGQ12824.

PTM databases

PhosphoSiteQ12824.

Proteomic databases

PRIDEQ12824.

Genome annotation databases

EnsemblENST00000263121; ENSP00000263121; ENSG00000099956; Homo sapiens. [Genome view]
GeneID6598.
KEGGhsa:6598.
UCSCuc002zyb.1. human.

Organism-specific databases

CTD6598.
GeneCardsGC22P022453.
H-InvDBHIX0016299.
HGNCHGNC:11103. SMARCB1.
HPACAB009196.
HPA018248.
HPA019127.
MIM162091. phenotype.
601607. gene.
609322. phenotype.
Orphanet93921. Neurofibromatosis, type 3.
69077. Rhabdoid tumor.
PharmGKBPA35953.
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG16826.
HOVERGENQ12824.

Gene expression databases

ArrayExpressQ12824.
BgeeQ12824.
CleanExHS_SMARCB1.
GenevestigatorQ12824.
GermOnlineENSG00000099956. Homo sapiens.

Family and domain databases

InterProIPR006939. SNF5.
IPR017393. SWI_SNF_chromatin_remodel_cplx.
[Graphical view]
PANTHERPTHR10019. SNF5. 1 hit.
PfamPF04855. SNF5. 2 hits.
[Graphical view]
PIRSFPIRSF038126. SWI_SNF. 1 hit.
ProtoNetSearch...

Other Resources

NextBio25665.
SOURCESearch...

Entry information

Entry nameSNF5_HUMAN
AccessionPrimary (citable) accession number: Q12824
Secondary accession number(s): O75784 expand/collapse secondary AC list , O95474, Q38GA1, Q76N08, Q9UBH2
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 16, 2004
Last modified: February 9, 2010
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

Human chromosome 22

Human chromosome 22: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents