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Protein

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

Gene

SMARCD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (PubMed:8804307). 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). Has a strong influence on vitamin D-mediated transcriptional activity from an enhancer vitamin D receptor element (VDRE). May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor (VDR) heterodimer (PubMed:14698202). Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation (PubMed:12917342).2 PublicationsBy similarity3 Publications

GO - Molecular functioni

  • chromatin binding Source: Ensembl
  • protein complex scaffold activity Source: UniProtKB
  • receptor binding Source: Ensembl
  • transcription coactivator activity Source: BHF-UCL

GO - Biological processi

  • cellular response to fatty acid Source: Ensembl
  • chromatin-mediated maintenance of transcription Source: UniProtKB
  • chromatin remodeling Source: BHF-UCL
  • covalent chromatin modification Source: UniProtKB-KW
  • nervous system development Source: UniProtKB-KW
  • nucleosome disassembly Source: BHF-UCL
  • regulation of transcription from RNA polymerase II promoter Source: BHF-UCL

Keywordsi

Molecular functionChromatin regulator
Biological processNeurogenesis

Enzyme and pathway databases

ReactomeiR-HSA-3214858. RMTs methylate histone arginines.
R-HSA-8939243. RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known.
SIGNORiQ96GM5.

Names & Taxonomyi

Protein namesi
Recommended name:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Alternative name(s):
60 kDa BRG-1/Brm-associated factor subunit A
BRG1-associated factor 60A
Short name:
BAF60A
SWI/SNF complex 60 kDa subunit
Gene namesi
Name:SMARCD1Imported
Synonyms:BAF60A1 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000066117.14.
HGNCiHGNC:11106. SMARCD1.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi6602.
OpenTargetsiENSG00000066117.
PharmGKBiPA35956.

Polymorphism and mutation databases

BioMutaiSMARCD1.
DMDMi238054318.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000719831 – 515SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1Add BLAST515

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei88Asymmetric dimethylarginineBy similarity1
Cross-linki101Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei223N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Ubl conjugation

Proteomic databases

EPDiQ96GM5.
MaxQBiQ96GM5.
PaxDbiQ96GM5.
PeptideAtlasiQ96GM5.
PRIDEiQ96GM5.

PTM databases

iPTMnetiQ96GM5.
PhosphoSitePlusiQ96GM5.

Expressioni

Tissue specificityi

Expressed in all tissues tested, including brain, heart, kidney, liver, lung, muscle, pancreas and placenta.1 Publication

Gene expression databases

BgeeiENSG00000066117.
CleanExiHS_SMARCD1.
ExpressionAtlasiQ96GM5. baseline and differential.
GenevisibleiQ96GM5. HS.

Organism-specific databases

HPAiHPA004101.

Interactioni

Subunit structurei

Component of the multiprotein chromatin-remodeling complexes SWI/SNF: SWI/SNF-A (BAF), SWI/SNF-B (PBAF) and related complexes. The canonical complex contains a catalytic subunit (either SMARCA4/BRG1/BAF190A or SMARCA2/BRM/BAF190B), and at least SMARCE1, ACTL6A/BAF53, SMARCC1/BAF155, SMARCC2/BAF170, and SMARCB1/SNF5/BAF47. Other subunits specific to each of the complexes may also be present permitting several possible combinations developmentally and tissue specific (PubMed:8895581). Component of the BAF complex, which includes at least actin (ACTB), ARID1A/BAF250A, ARID1B/BAF250B, SMARCA2/BRM, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C (PubMed:18765789). In muscle cells, the BAF complex also contains DPF3. 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). Component of the SWI/SNF-B (PBAF) chromatin remodeling complex, at least composed of SMARCA4/BRG1, SMARCB1/BAF47/SNF5, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, perhaps SMARCD3/BAF60C, SMARCC1/BAF155, SMARCC2/BAF170, PBRM1/BAF180, ARID2/BAF200 and actin (ACTB) (PubMed:22952240, PubMed:26601204). Specifically interacts with the VDR heterodimer complex (PubMed:14698202). Interacts with ESR1, NR3C1, NR1H4, PGR, SMARCA4, SMARCC1 and SMARCC2 (PubMed:12917342).2 PublicationsBy similarity4 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • protein complex scaffold activity Source: UniProtKB
  • receptor binding Source: Ensembl

Protein-protein interaction databases

BioGridi112486. 116 interactors.
CORUMiQ96GM5.
DIPiDIP-33390N.
IntActiQ96GM5. 111 interactors.
MINTiMINT-1144212.
STRINGi9606.ENSP00000378414.

Structurei

3D structure databases

ProteinModelPortaliQ96GM5.
SMRiQ96GM5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini291 – 390SWIBAdd BLAST100

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni43 – 167Interaction with ESR1, NR1H4, NR3C1, PGR and SMARCA41 PublicationAdd BLAST125
Regioni168 – 474Interaction with SMARCC1 and SMARCC21 PublicationAdd BLAST307
Regioni180 – 515Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin; required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivoAdd BLAST336

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili412 – 440Sequence analysisAdd BLAST29

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi124 – 127Poly-Lys4

Sequence similaritiesi

Belongs to the SMARCD family.Sequence analysis

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2570. Eukaryota.
COG5531. LUCA.
GeneTreeiENSGT00390000017809.
HOGENOMiHOG000240746.
HOVERGENiHBG054046.
InParanoidiQ96GM5.
KOiK11650.
OMAiFRLPWVE.
OrthoDBiEOG091G06WW.
PhylomeDBiQ96GM5.
TreeFamiTF106486.

Family and domain databases

Gene3Di1.10.245.10. 1 hit.
InterProiView protein in InterPro
IPR019835. SWIB_domain.
IPR036885. SWIB_MDM2_dom_sf.
IPR003121. SWIB_MDM2_domain.
PfamiView protein in Pfam
PF02201. SWIB. 1 hit.
SMARTiView protein in SMART
SM00151. SWIB. 1 hit.
SUPFAMiSSF47592. SSF47592. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 11 Publication (identifier: Q96GM5-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MAARAGFQSV APSGGAGASG GAGAAAALGP GGTPGPPVRM GPAPGQGLYR
60 70 80 90 100
SPMPGAAYPR PGMLPGSRMT PQGPSMGPPG YGGNPSVRPG LAQSGMDQSR
110 120 130 140 150
KRPAPQQIQQ VQQQAVQNRN HNAKKKKMAD KILPQRIREL VPESQAYMDL
160 170 180 190 200
LAFERKLDQT IMRKRLDIQE ALKRPIKQKR KLRIFISNTF NPAKSDAEDG
210 220 230 240 250
EGTVASWELR VEGRLLEDSA LSKYDATKQK RKFSSFFKSL VIELDKDLYG
260 270 280 290 300
PDNHLVEWHR TATTQETDGF QVKRPGDVNV RCTVLLMLDY QPPQFKLDPR
310 320 330 340 350
LARLLGIHTQ TRPVIIQALW QYIKTHKLQD PHEREFVICD KYLQQIFESQ
360 370 380 390 400
RMKFSEIPQR LHALLMPPEP IIINHVISVD PNDQKKTACY DIDVEVDDTL
410 420 430 440 450
KTQMNSFLLS TASQQEIATL DNKIHETIET INQLKTQREF MLSFARDPQG
460 470 480 490 500
FINDWLQSQC RDLKTMTDVV GNPEEERRAE FYFQPWAQEA VCRYFYSKVQ
510
QRRQELEQAL GIRNT
Length:515
Mass (Da):58,233
Last modified:May 26, 2009 - v2
Checksum:iE683AA1E345DA400
GO
Isoform 21 Publication (identifier: Q96GM5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     423-463: Missing.

Note: No experimental confirmation available.
Show »
Length:474
Mass (Da):53,299
Checksum:i2DA7AB84B9A3F933
GO

Sequence cautioni

The sequence AAC50695 differs from that shown. Reason: Frameshift at position 30.Curated
The sequence AAD23390 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAH09368 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti349S → T in AAC50695 (PubMed:8804307).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_004179423 – 463Missing in isoform 2. 1 PublicationAdd BLAST41

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF109733 mRNA. Translation: AAD23390.1. Different initiation.
U66617 mRNA. Translation: AAC50695.1. Frameshift.
AC025154 Genomic DNA. No translation available.
BC009368 mRNA. Translation: AAH09368.3. Different initiation.
CCDSiCCDS8797.2. [Q96GM5-1]
CCDS8798.2. [Q96GM5-2]
RefSeqiNP_003067.3. NM_003076.4. [Q96GM5-1]
NP_620710.2. NM_139071.2. [Q96GM5-2]
UniGeneiHs.79335.

Genome annotation databases

EnsembliENST00000381513; ENSP00000370924; ENSG00000066117. [Q96GM5-2]
ENST00000394963; ENSP00000378414; ENSG00000066117. [Q96GM5-1]
GeneIDi6602.
KEGGihsa:6602.
UCSCiuc001rvx.5. human. [Q96GM5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiSMRD1_HUMAN
AccessioniPrimary (citable) accession number: Q96GM5
Secondary accession number(s): A6NN27, Q92924, Q9Y635
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 17, 2003
Last sequence update: May 26, 2009
Last modified: November 22, 2017
This is version 155 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families