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Q6STE5 (SMRD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3
Alternative name(s):
60 kDa BRG-1/Brm-associated factor subunit C
BRG1-associated factor 60C
Short name=BAF60C
Gene names
Name:SMARCD3
Synonyms:BAF60C
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length483 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Plays a role in ATP dependent nucleosome remodeling by SMARCA4 containing complexes. Stimulates nuclear receptor mediated transcription. 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. Ref.1

Subunit structure

Component of the BAF 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. Interacts with SMARCA4/BRG1/BAF190A, the catalytic subunit of the SWI/SNF related nucleosome-remodeling complexes BRG1(I) and BRG1(II). The precise distribution of the related SMARCD1, SMARCD2 and SMARCD3 proteins among these and other SWI/SNF nucleosome-remodeling complexes is not fully known. Also interacts with several nuclear receptors including PPARG/NR1C3, RXRA/NR1F1, ESR1, NR5A1, NR5A2/LRH1 and other transcriptional activators including the HLH protein SREBF1/SREBP1 and the homeobox protein PBX1. May allow recruitment of Swi/SNF containing complexes specifically to promoters where these factors are located. 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.2 Ref.7

Subcellular location

Nucleus Ref.2.

Tissue specificity

Isoform 2 and isoform 1 are expressed in brain, heart, kidney, placenta, prostate, salivary gland, spleen, testis, thyroid, trachea and uterus. Isoform 1 is also expressed in skeletal muscle and adipose tissue.

Sequence similarities

Belongs to the SMARCD family.

Contains 1 SWIB domain.

Sequence caution

The sequence AAC50697.1 differs from that shown. Reason: Frameshift at positions 41, 65 and 78.

Ontologies

Keywords
   Biological processNeurogenesis
Transcription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   Molecular functionChromatin regulator
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcardiac right ventricle formation

Inferred from electronic annotation. Source: Ensembl

cellular lipid metabolic process

Traceable author statement. Source: Reactome

chromatin remodeling

Inferred from direct assay PubMed 11726552. Source: BHF-UCL

muscle cell differentiation

Inferred from electronic annotation. Source: Ensembl

neural retina development

Inferred from expression pattern PubMed 18816825. Source: BHF-UCL

nucleosome disassembly

Inferred from direct assay PubMed 8895581. Source: BHF-UCL

positive regulation of neuroblast proliferation

Inferred from direct assay PubMed 18816825. Source: BHF-UCL

positive regulation of transcription, DNA-templated

Inferred from direct assay Ref.2. Source: UniProtKB

regulation of protein binding

Inferred from electronic annotation. Source: Ensembl

regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 17363140PubMed 17363140. Source: BHF-UCL

secondary heart field specification

Inferred from electronic annotation. Source: Ensembl

small molecule metabolic process

Traceable author statement. Source: Reactome

transcription, DNA-templated

Inferred from direct assay Ref.2. Source: UniProtKB

   Cellular_componentSWI/SNF complex

Non-traceable author statement Ref.2. Source: UniProtKB

cytoplasm

Inferred from direct assay PubMed 17363140PubMed 17363140. Source: BHF-UCL

nBAF complex

Inferred from sequence or structural similarity. Source: UniProtKB

npBAF complex

Inferred from sequence or structural similarity. Source: UniProtKB

nuclear chromatin

Inferred from direct assay PubMed 17363140. Source: BHF-UCL

nucleoplasm

Traceable author statement. Source: Reactome

nucleus

Inferred from direct assay PubMed 17363140PubMed 17363140. Source: BHF-UCL

   Molecular_functionligand-dependent nuclear receptor binding

Inferred from physical interaction PubMed 17363140PubMed 17363140. Source: BHF-UCL

ligand-dependent nuclear receptor transcription coactivator activity

Inferred from mutant phenotype PubMed 17363140PubMed 17363140. Source: BHF-UCL

nuclear hormone receptor binding

Inferred from physical interaction Ref.2. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.2. Source: IntAct

receptor binding

Inferred from physical interaction Ref.2. Source: UniProtKB

transcription coactivator activity

Non-traceable author statement Ref.1. Source: BHF-UCL

transcription factor binding

Inferred from physical interaction Ref.2. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PPARGP372313EBI-488511,EBI-781384

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q6STE5-1)

Also known as: BAF60C2;

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 2 (identifier: Q6STE5-2)

Also known as: BAF60C1;

The sequence of this isoform differs from the canonical sequence as follows:
     1-26: MAADEVAGGARKATKSKLFEFLVHGV → MTPGLQHPPTVVQ

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.9
Chain2 – 483482SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3
PRO_0000071988

Regions

Domain259 – 33476SWIB

Amino acid modifications

Modified residue21N-acetylalanine Ref.9
Modified residue1781Phosphoserine Ref.6

Natural variations

Alternative sequence1 – 2626MAADE…LVHGV → MTPGLQHPPTVVQ in isoform 2.
VSP_012498
Natural variant1701P → S. Ref.2
Corresponds to variant rs1050101 [ dbSNP | Ensembl ].
VAR_020884

Experimental info

Sequence conflict881V → E in AAC50697. Ref.1
Sequence conflict1401R → G in AAC50697. Ref.1
Sequence conflict3871A → P in AAC50697. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (BAF60C2) [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: B7B28DD11DCD0B5C

FASTA48355,016
        10         20         30         40         50         60 
MAADEVAGGA RKATKSKLFE FLVHGVRPGM PSGARMPHQG APMGPPGSPY MGSPAVRPGL 

        70         80         90        100        110        120 
APAGMEPARK RAAPPPGQSQ AQSQGQPVPT APARSRSAKR RKMADKILPQ RIRELVPESQ 

       130        140        150        160        170        180 
AYMDLLAFER KLDQTIMRKR VDIQEALKRP MKQKRKLRLY ISNTFNPAKP DAEDSDGSIA 

       190        200        210        220        230        240 
SWELRVEGKL LDDPSKQKRK FSSFFKSLVI ELDKDLYGPD NHLVEWHRTP TTQETDGFQV 

       250        260        270        280        290        300 
KRPGDLSVRC TLLLMLDYQP PQFKLDPRLA RLLGLHTQSR SAIVQALWQY VKTNRLQDSH 

       310        320        330        340        350        360 
DKEYINGDKY FQQIFDCPRL KFSEIPQRLT ALLLPPDPIV INHVISVDPS DQKKTACYDI 

       370        380        390        400        410        420 
DVEVEEPLKG QMSSFLLSTA NQQEISALDS KIHETIESIN QLKIQRDFML SFSRDPKGYV 

       430        440        450        460        470        480 
QDLLRSQSRD LKVMTDVAGN PEEERRAEFY HQPWSQEAVS RYFYCKIQQR RQELEQSLVV 


RNT 

« Hide

Isoform 2 (BAF60C1) [UniParc].

Checksum: DD6C2454B7AC2B04
Show »

FASTA47053,687

References

« Hide 'large scale' references
[1]"Diversity and specialization of mammalian SWI/SNF complexes."
Wang W., Xue Y., Zhou S., Kuo A., Cairns B.R., Crabtree G.R.
Genes Dev. 10:2117-2130(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION.
[2]"Transcription factors and nuclear receptors interact with the SWI/SNF complex through the BAF60c subunit."
Debril M.-B., Gelman L., Fayard E., Annicotte J.-S., Rocchi S., Auwerx J.
J. Biol. Chem. 279:16677-16686(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), SUBCELLULAR LOCATION, INTERACTION WITH SMARCA4 AND TRANSCRIPTIONAL ACTIVATORS, VARIANT SER-170.
Tissue: Adipose tissue.
[3]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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 2).
Tissue: Blood and Uterus.
[6]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-178, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE BAF COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
[8]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U66619 mRNA. Translation: AAC50697.1. Frameshift.
AY450430 mRNA. Translation: AAR88510.1.
AY450431 mRNA. Translation: AAR88511.1.
AC021097 Genomic DNA. Translation: AAS00380.1.
AC005486 Genomic DNA. Translation: AAS02031.1.
CH471173 Genomic DNA. Translation: EAW54005.1.
CH471173 Genomic DNA. Translation: EAW54007.1.
CH471173 Genomic DNA. Translation: EAW54008.1.
BC002628 mRNA. Translation: AAH02628.1.
BC110350 mRNA. Translation: AAI10351.1.
CCDSCCDS34780.1. [Q6STE5-1]
CCDS5924.1. [Q6STE5-2]
RefSeqNP_001003801.1. NM_001003801.1. [Q6STE5-1]
NP_001003802.1. NM_001003802.1. [Q6STE5-2]
NP_003069.2. NM_003078.3. [Q6STE5-2]
UniGeneHs.647067.

3D structure databases

ProteinModelPortalQ6STE5.
SMRQ6STE5. Positions 259-338.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112488. 23 interactions.
DIPDIP-33012N.
IntActQ6STE5. 4 interactions.
STRING9606.ENSP00000262188.

PTM databases

PhosphoSiteQ6STE5.

Polymorphism databases

DMDM57013057.

Proteomic databases

MaxQBQ6STE5.
PaxDbQ6STE5.
PRIDEQ6STE5.

Protocols and materials databases

DNASU6604.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000262188; ENSP00000262188; ENSG00000082014. [Q6STE5-1]
ENST00000356800; ENSP00000349254; ENSG00000082014. [Q6STE5-2]
ENST00000392811; ENSP00000376558; ENSG00000082014. [Q6STE5-2]
GeneID6604.
KEGGhsa:6604.
UCSCuc003wjs.3. human. [Q6STE5-1]
uc003wjt.3. human. [Q6STE5-2]

Organism-specific databases

CTD6604.
GeneCardsGC07M150935.
HGNCHGNC:11108. SMARCD3.
MIM601737. gene.
neXtProtNX_Q6STE5.
PharmGKBPA35958.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5531.
HOVERGENHBG054046.
InParanoidQ6STE5.
KOK11650.
OMARAAFYHE.
PhylomeDBQ6STE5.
TreeFamTF106486.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.

Gene expression databases

ArrayExpressQ6STE5.
BgeeQ6STE5.
CleanExHS_SMARCD3.
GenevestigatorQ6STE5.

Family and domain databases

Gene3D1.10.245.10. 1 hit.
InterProIPR019835. SWIB_domain.
IPR003121. SWIB_MDM2_domain.
[Graphical view]
PfamPF02201. SWIB. 1 hit.
[Graphical view]
SMARTSM00151. SWIB. 1 hit.
[Graphical view]
SUPFAMSSF47592. SSF47592. 1 hit.
ProtoNetSearch...

Other

ChiTaRSSMARCD3. human.
GeneWikiSMARCD3.
GenomeRNAi6604.
NextBio25695.
PROQ6STE5.
SOURCESearch...

Entry information

Entry nameSMRD3_HUMAN
AccessionPrimary (citable) accession number: Q6STE5
Secondary accession number(s): D3DX10 expand/collapse secondary AC list , Q2YD86, Q75MJ2, Q75MR8, Q92926, Q9BUH1
Entry history
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: July 5, 2004
Last modified: July 9, 2014
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
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

SIMILARITY comments

Index of protein domains and families

MIM cross-references

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

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM