Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

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

Gene

Smarcd1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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 (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 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 (PubMed:17640523). 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 similarity).By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator
Biological processNeurogenesis

Enzyme and pathway databases

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

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
Protein D15KZ1
SWI/SNF complex 60 kDa subunit
Gene namesi
Name:Smarcd1
Synonyms:Baf60a, D15Kz1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:1933623 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000719841 – 515SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1Add BLAST515

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei68Asymmetric dimethylarginineBy similarity1
Modified residuei88Asymmetric dimethylarginineCombined sources1
Cross-linki101Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei203PhosphothreonineBy similarity1
Modified residuei223N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ61466
PeptideAtlasiQ61466
PRIDEiQ61466

PTM databases

iPTMnetiQ61466
PhosphoSitePlusiQ61466

Expressioni

Tissue specificityi

Ubiquitous.2 Publications

Developmental stagei

Expressed ubiquitously throughout the developing spinal cord, brain and other embryonic tissues at E10.5-E16.5.1 Publication

Gene expression databases

BgeeiENSMUSG00000023018
GenevisibleiQ61466 MM

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:8804307, 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 (By similarity). 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 (PubMed:17640523). 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). Specifically interacts with the VDR heterodimer complex. Interacts with ESR1, NR3C1, NR1H4, PGR, SMARCA4, SMARCC1 and SMARCC2 (By similarity).By similarity3 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

Protein-protein interaction databases

BioGridi21997715 interactors.
CORUMiQ61466
DIPiDIP-33019N
IntActiQ61466 14 interactors.
MINTiQ61466
STRINGi10090.ENSMUSP00000023759

Structurei

Secondary structure

1515
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi294 – 297Combined sources4
Helixi301 – 304Combined sources4
Beta strandi308 – 311Combined sources4
Helixi312 – 325Combined sources14
Beta strandi334 – 337Combined sources4
Helixi343 – 346Combined sources4
Beta strandi350 – 353Combined sources4
Helixi354 – 356Combined sources3
Helixi358 – 364Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UHRNMR-A291-370[»]
ProteinModelPortaliQ61466
SMRiQ61466
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ61466

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 SMARCA4By similarityAdd BLAST125
Regioni168 – 474Interaction with SMARCC1 and SMARCC2By similarityAdd BLAST307
Regioni180 – 515Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin; required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivoBy similarityAdd 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.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2570 Eukaryota
COG5531 LUCA
GeneTreeiENSGT00390000017809
HOGENOMiHOG000240746
HOVERGENiHBG054046
InParanoidiQ61466
OMAiFRLPWVE
OrthoDBiEOG091G06WW
PhylomeDBiQ61466
TreeFamiTF106486

Family and domain databases

Gene3Di1.10.245.101 hit
InterProiView protein in InterPro
IPR038041 SMARCD1
IPR019835 SWIB_domain
IPR036885 SWIB_MDM2_dom_sf
IPR003121 SWIB_MDM2_domain
PANTHERiPTHR13844:SF1 PTHR13844:SF1, 1 hit
PfamiView protein in Pfam
PF02201 SWIB, 1 hit
SMARTiView protein in SMART
SM00151 SWIB, 1 hit
SUPFAMiSSF47592 SSF47592, 1 hit

Sequencei

Sequence statusi: Complete.

Q61466-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAARAGFQSV APSGGAGASG GAGVAAALGP 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 VEGRLLEDAA LSKYDATKQK RKFSSFFKSL VIELDKDLYG
260 270 280 290 300
PDNHLVEWHR TATTQETDGF QVKRPGDVNV RCTVLLMLDY QPPQFKLDPR
310 320 330 340 350
LARLLGIHTQ TRPVIIQALW QYIKTHKLQD PHEREFVLCD 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):58,245
Last modified:May 26, 2009 - v3
Checksum:i166D88566C856A0F
GO

Sequence cautioni

The sequence AAA53377 differs from that shown. Reason: Frameshift at positions 29, 445, 447, 462 and 473.Curated
The sequence AAA53377 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAC52794 differs from that shown. Reason: Frameshift at positions 29, 445 and 447.Curated
The sequence AAC52794 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAH26783 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti15G → A in AAA53377 (PubMed:2725507).Curated1
Sequence conflicti15G → A in AAC52794 (PubMed:8804307).Curated1
Sequence conflicti215L → I in BAC35856 (PubMed:16141072).Curated1
Sequence conflicti218D → E in BAC35856 (PubMed:16141072).Curated1
Sequence conflicti449Q → S in AAA53377 (PubMed:2725507).Curated1
Sequence conflicti449Q → S in AAC52794 (PubMed:8804307).Curated1
Sequence conflicti462D → G in AAA53377 (PubMed:2725507).Curated1
Sequence conflicti462D → G in AAC52794 (PubMed:8804307).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC026783 mRNA Translation: AAH26783.3 Different initiation.
BC059921 mRNA No translation available.
M25773 mRNA Translation: AAA53377.1 Sequence problems.
U66620 mRNA Translation: AAC52794.1 Sequence problems.
AK075611 mRNA Translation: BAC35856.1
CCDSiCCDS37204.1
PIRiA30222
RefSeqiNP_114030.2, NM_031842.2
UniGeneiMm.273756

Genome annotation databases

EnsembliENSMUST00000023759; ENSMUSP00000023759; ENSMUSG00000023018
GeneIDi83797
UCSCiuc007xqb.1 mouse

Similar proteinsi

Entry informationi

Entry nameiSMRD1_MOUSE
AccessioniPrimary (citable) accession number: Q61466
Secondary accession number(s): P70384, Q8R0I7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 26, 2009
Last modified: April 25, 2018
This is version 145 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome