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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 chromatin remodeling. 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). 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. Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation.By similarity3 Publications

GO - Molecular functioni

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

GO - Biological processi

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

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

Neurogenesis

Enzyme and pathway databases

BioCyciZFISH:ENSG00000066117-MONOMER.
ReactomeiR-HSA-3214858. RMTs methylate histone arginines.
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

HGNCiHGNC:11106. SMARCD1.

Subcellular locationi

GO - Cellular componenti

  • nBAF complex Source: UniProtKB
  • npBAF complex Source: UniProtKB
  • SWI/SNF complex Source: UniProtKB
Complete GO annotation...

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
Modified residuei223N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Methylation

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 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. Specifically interacts with the VDR heterodimer complex. Interacts with ESR1, NR3C1, NR1H4, PGR, SMARCA4, SMARCC1 and SMARCC2. 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).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
KRT15P190123EBI-358489,EBI-739566
LDOC1O957513EBI-358489,EBI-740738
MED4Q9NPJ63EBI-358489,EBI-394607
Nr3c1P065362EBI-358489,EBI-1187143From a different organism.
SMARCA4P515327EBI-358489,EBI-302489
SMARCC1Q929224EBI-358489,EBI-355653
USHBP1Q8N6Y03EBI-358489,EBI-739895
VPS37BQ9H9H46EBI-358489,EBI-4400866

GO - Molecular functioni

  • protein complex scaffold Source: UniProtKB

Protein-protein interaction databases

BioGridi112486. 113 interactors.
DIPiDIP-33390N.
IntActiQ96GM5. 89 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
Contains 1 SWIB domain.Sequence analysis

Keywords - Domaini

Coiled coil

Phylogenomic databases

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

Family and domain databases

Gene3Di1.10.245.10. 1 hit.
InterProiIPR019835. SWIB_domain.
IPR003121. SWIB_MDM2_domain.
[Graphical view]
PfamiPF02201. SWIB. 1 hit.
[Graphical view]
SMARTiSM00151. SWIB. 1 hit.
[Graphical view]
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.Curated
The sequence AAH09368 differs from that shown. Reason: Erroneous initiation.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

Cross-referencesi

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.

3D structure databases

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

Protein-protein interaction databases

BioGridi112486. 113 interactors.
DIPiDIP-33390N.
IntActiQ96GM5. 89 interactors.
MINTiMINT-1144212.
STRINGi9606.ENSP00000378414.

PTM databases

iPTMnetiQ96GM5.
PhosphoSitePlusiQ96GM5.

Polymorphism and mutation databases

BioMutaiSMARCD1.
DMDMi238054318.

Proteomic databases

EPDiQ96GM5.
MaxQBiQ96GM5.
PaxDbiQ96GM5.
PeptideAtlasiQ96GM5.
PRIDEiQ96GM5.

Protocols and materials databases

DNASUi6602.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi6602.
DisGeNETi6602.
GeneCardsiSMARCD1.
HGNCiHGNC:11106. SMARCD1.
HPAiHPA004101.
MIMi601735. gene.
neXtProtiNX_Q96GM5.
OpenTargetsiENSG00000066117.
PharmGKBiPA35956.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000066117-MONOMER.
ReactomeiR-HSA-3214858. RMTs methylate histone arginines.
SIGNORiQ96GM5.

Miscellaneous databases

ChiTaRSiSMARCD1. human.
GeneWikiiSMARCD1.
GenomeRNAii6602.
PROiQ96GM5.
SOURCEiSearch...

Gene expression databases

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

Family and domain databases

Gene3Di1.10.245.10. 1 hit.
InterProiIPR019835. SWIB_domain.
IPR003121. SWIB_MDM2_domain.
[Graphical view]
PfamiPF02201. SWIB. 1 hit.
[Graphical view]
SMARTiSM00151. SWIB. 1 hit.
[Graphical view]
SUPFAMiSSF47592. SSF47592. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSMRD1_HUMAN
AccessioniPrimary (citable) accession number: Q96GM5
Secondary accession number(s): A6NN27, Q92924, Q9Y635
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 17, 2003
Last sequence update: May 26, 2009
Last modified: November 30, 2016
This is version 146 of the entry and version 2 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.