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Protein

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3

Gene

Smarcd3

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 (PubMed:22952240, PubMed:26601204). 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 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).2 PublicationsBy similarity1 Publication

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator
Biological processNeurogenesis, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-MMU-3214858 RMTs methylate histone arginines
R-MMU-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
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 3
Alternative name(s):
60 kDa BRG-1/Brm-associated factor subunit C
BRG1-associated factor 60C
Short name:
BAF60C
Short name:
mBAF60c
Gene namesi
Name:Smarcd3
Synonyms:Baf60c
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:1914243 Smarcd3

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
Initiator methionineiRemovedBy similarity
ChainiPRO_00000719892 – 483SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3Add BLAST482

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei178PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ6P9Z1
PaxDbiQ6P9Z1
PeptideAtlasiQ6P9Z1
PRIDEiQ6P9Z1

PTM databases

iPTMnetiQ6P9Z1
PhosphoSitePlusiQ6P9Z1

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiENSMUSG00000028949 Expressed in 269 organ(s), highest expression level in gastrocnemius
ExpressionAtlasiQ6P9Z1 baseline and differential
GenevisibleiQ6P9Z1 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 (Probable). 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. In muscle cells, the BAF complex also contains DPF3 (By similarity). 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). May be a 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 (PubMed:22952240, PubMed:26601204). Component of SWI/SNF (GBAF) subcomplex, which includes at least BICRA or BICRAL (mutually exclusive), BRD9, SS18, SMARCA2/BRM, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, SMARCC1/BAF155, and SMARCD1/BAF60A (PubMed:29374058). Interacts with SMARCA4/BRG1/BAF190A. The precise distribution of the related SMARCD1, SMARCD2 and SMARCD3 proteins among these and other SWI/SNF nucleosome-remodeling complexes is not fully known. May allow recruitment of SWI/SNF containing complexes specifically to promoters where these factors are located. 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 (By similarity).2 PublicationsBy similarity2 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi211860, 9 interactors
ComplexPortaliCPX-1232 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA2 variant
CPX-1233 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA4 variant
CPX-1234 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA2 variant
CPX-1235 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA4 variant
CPX-1236 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA2 variant
CPX-1237 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA4 variant
CPX-1238 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA2 variant
CPX-1239 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA4 variant
CPX-1240 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA2 variant
CPX-1241 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA4 variant
CPX-1242 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA2 variant
CPX-1243 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA4 variant
CPX-1244 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA2 variant
CPX-1245 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA4 variant
CPX-1246 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA2 variant
CPX-1247 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA4 variant
CPX-1252 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
CPX-1253 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
CPX-1254 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
CPX-1255 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
CPX-1256 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
CPX-1257 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
CPX-1258 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
CPX-1259 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
CORUMiQ6P9Z1
DIPiDIP-48886N
IntActiQ6P9Z1, 6 interactors
MINTiQ6P9Z1
STRINGi10090.ENSMUSP00000030791

Structurei

3D structure databases

ProteinModelPortaliQ6P9Z1
SMRiQ6P9Z1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini259 – 334SWIBAdd BLAST76

Sequence similaritiesi

Belongs to the SMARCD family.Curated

Phylogenomic databases

eggNOGiKOG2570 Eukaryota
COG5531 LUCA
GeneTreeiENSGT00390000017809
HOGENOMiHOG000240746
HOVERGENiHBG054046
InParanoidiQ6P9Z1
KOiK11650
OrthoDBiEOG091G06WW
PhylomeDBiQ6P9Z1
TreeFamiTF106486

Family and domain databases

Gene3Di1.10.245.10, 1 hit
InterProiView protein in InterPro
IPR038043 SMARCD3
IPR019835 SWIB_domain
IPR036885 SWIB_MDM2_dom_sf
IPR003121 SWIB_MDM2_domain
PANTHERiPTHR13844:SF5 PTHR13844:SF5, 1 hit
PfamiView protein in Pfam
PF02201 SWIB, 1 hit
SMARTiView protein in SMART
SM00151 SWIB, 1 hit
SUPFAMiSSF47592 SSF47592, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q6P9Z1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAADEVAGGA RKATKSKLFE FLVHGVRPGM PSGARMPHQG APMGPPGSPY
60 70 80 90 100
MGSPAVRPGL APAGMEPARK RAAPPPGQSQ AQGQGQPVPT APARSRSAKR
110 120 130 140 150
RKMADKILPQ RIRELVPESQ AYMDLLAFER KLDQTIMRKR VDIQEALKRP
160 170 180 190 200
MKQKRKLRLY ISNTFNPAKP DAEDSDGSIA SWELRVEGKL LDDPSKQKRK
210 220 230 240 250
FSSFFKSLVI ELDKDLYGPD NHLVEWHRTP TTQETDGFQV KRPGDLSVRC
260 270 280 290 300
TLLLMLDYQP PQFKLDPRLA RLLGLHTQSR SAIVQALWQY VKTNRLQDSH
310 320 330 340 350
DKEYINGDKY FQQIFDCPRL KFSEIPQRLT ALLLPPDPIV INHVISVDPS
360 370 380 390 400
DQKKTACYDI DVEVEEPLKG QMSSFLLSTA NQQEISALDS KIHETIESIN
410 420 430 440 450
QLKIQRDFML SFSRDPKGYV QDLLRSQSRD LKVMTDVAGN PEEERRAEFY
460 470 480
HQPWSQEAVS RYFYCKIQQR RQELEQSLVV RNT
Length:483
Mass (Da):54,986
Last modified:January 4, 2005 - v2
Checksum:i70A1928E8F0A03C0
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A0G2JG60A0A0G2JG60_MOUSE
SWI/SNF related, matrix associated,...
Smarcd3 mCG_16507
454Annotation score:

Sequence cautioni

The sequence BAB23813 differs from that shown. Reason: Frameshift at position 91.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti151M → I in AAH60525 (PubMed:15489334).Curated1
Sequence conflicti323S → C in BAB23813 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK005094 mRNA Translation: BAB23813.1 Frameshift.
AK019374 mRNA Translation: BAB31685.2
BC013122 mRNA Translation: AAH13122.2
BC060525 mRNA Translation: AAH60525.1
CCDSiCCDS19126.1
RefSeqiNP_080167.3, NM_025891.3
UniGeneiMm.436539

Genome annotation databases

EnsembliENSMUST00000030791; ENSMUSP00000030791; ENSMUSG00000028949
GeneIDi66993
KEGGimmu:66993
UCSCiuc008wsd.1 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK005094 mRNA Translation: BAB23813.1 Frameshift.
AK019374 mRNA Translation: BAB31685.2
BC013122 mRNA Translation: AAH13122.2
BC060525 mRNA Translation: AAH60525.1
CCDSiCCDS19126.1
RefSeqiNP_080167.3, NM_025891.3
UniGeneiMm.436539

3D structure databases

ProteinModelPortaliQ6P9Z1
SMRiQ6P9Z1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi211860, 9 interactors
ComplexPortaliCPX-1232 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA2 variant
CPX-1233 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA4 variant
CPX-1234 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA2 variant
CPX-1235 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA4 variant
CPX-1236 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA2 variant
CPX-1237 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA4 variant
CPX-1238 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA2 variant
CPX-1239 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA4 variant
CPX-1240 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA2 variant
CPX-1241 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA4 variant
CPX-1242 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA2 variant
CPX-1243 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA4 variant
CPX-1244 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA2 variant
CPX-1245 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA4 variant
CPX-1246 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA2 variant
CPX-1247 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA4 variant
CPX-1252 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
CPX-1253 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
CPX-1254 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
CPX-1255 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
CPX-1256 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
CPX-1257 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
CPX-1258 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
CPX-1259 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
CORUMiQ6P9Z1
DIPiDIP-48886N
IntActiQ6P9Z1, 6 interactors
MINTiQ6P9Z1
STRINGi10090.ENSMUSP00000030791

PTM databases

iPTMnetiQ6P9Z1
PhosphoSitePlusiQ6P9Z1

Proteomic databases

MaxQBiQ6P9Z1
PaxDbiQ6P9Z1
PeptideAtlasiQ6P9Z1
PRIDEiQ6P9Z1

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000030791; ENSMUSP00000030791; ENSMUSG00000028949
GeneIDi66993
KEGGimmu:66993
UCSCiuc008wsd.1 mouse

Organism-specific databases

CTDi6604
MGIiMGI:1914243 Smarcd3

Phylogenomic databases

eggNOGiKOG2570 Eukaryota
COG5531 LUCA
GeneTreeiENSGT00390000017809
HOGENOMiHOG000240746
HOVERGENiHBG054046
InParanoidiQ6P9Z1
KOiK11650
OrthoDBiEOG091G06WW
PhylomeDBiQ6P9Z1
TreeFamiTF106486

Enzyme and pathway databases

ReactomeiR-MMU-3214858 RMTs methylate histone arginines
R-MMU-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-MMU-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known

Miscellaneous databases

PROiPR:Q6P9Z1
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000028949 Expressed in 269 organ(s), highest expression level in gastrocnemius
ExpressionAtlasiQ6P9Z1 baseline and differential
GenevisibleiQ6P9Z1 MM

Family and domain databases

Gene3Di1.10.245.10, 1 hit
InterProiView protein in InterPro
IPR038043 SMARCD3
IPR019835 SWIB_domain
IPR036885 SWIB_MDM2_dom_sf
IPR003121 SWIB_MDM2_domain
PANTHERiPTHR13844:SF5 PTHR13844:SF5, 1 hit
PfamiView protein in Pfam
PF02201 SWIB, 1 hit
SMARTiView protein in SMART
SM00151 SWIB, 1 hit
SUPFAMiSSF47592 SSF47592, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSMRD3_MOUSE
AccessioniPrimary (citable) accession number: Q6P9Z1
Secondary accession number(s): Q921D3, Q9CX89, Q9DB99
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: November 7, 2018
This is version 130 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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