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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: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in chromatin remodeling. 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. 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 similarity1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

Neurogenesis

Enzyme and pathway databases

ReactomeiR-MMU-3214858. RMTs methylate histone arginines.

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:1933623. Smarcd1.

Subcellular locationi

GO - Cellular componenti

  • BAF-type complex Source: MGI
  • nBAF complex Source: UniProtKB
  • npBAF complex Source: UniProtKB
  • SWI/SNF complex Source: MGI
Complete GO annotation...

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 residuei88Asymmetric dimethylarginineCombined sources1
Modified residuei223N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation, Methylation

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 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 (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 similarity3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Akirin2B1AXD82EBI-371529,EBI-10107866
Smarcc1P974963EBI-371529,EBI-648047
Tp53P023404EBI-371529,EBI-474016

GO - Molecular functioni

Protein-protein interaction databases

BioGridi219977. 15 interactors.
DIPiDIP-33019N.
IntActiQ61466. 9 interactors.
MINTiMINT-4134901.
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
Contains 1 SWIB domain.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2570. Eukaryota.
COG5531. LUCA.
GeneTreeiENSGT00390000017809.
HOGENOMiHOG000240746.
HOVERGENiHBG054046.
InParanoidiQ61466.
KOiK11650.
OMAiQQPAFQS.
OrthoDBiEOG091G06WW.
PhylomeDBiQ61466.
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 2 (identifier: Q61466-1) [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 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
Isoform 1 (identifier: Q61466-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     444-449: FARDPQ → LPEPS

Show »
Length:514
Mass (Da):58,053
Checksum:i12CEDD9D210D8A31
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.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

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_004180444 – 449FARDPQ → LPEPS in isoform 1. 2 Publications6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M25773 mRNA. Translation: AAA53377.1. Sequence problems.
U66620 mRNA. Translation: AAC52794.1. Sequence problems.
BC026783 mRNA. Translation: AAH26783.3. Different initiation.
BC059921 mRNA. No translation available.
AK075611 mRNA. Translation: BAC35856.1.
CCDSiCCDS37204.1. [Q61466-1]
PIRiA30222.
RefSeqiNP_114030.2. NM_031842.2. [Q61466-1]
UniGeneiMm.273756.

Genome annotation databases

EnsembliENSMUST00000023759; ENSMUSP00000023759; ENSMUSG00000023018. [Q61466-1]
GeneIDi83797.
KEGGimmu:83797.
UCSCiuc007xqb.1. mouse. [Q61466-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M25773 mRNA. Translation: AAA53377.1. Sequence problems.
U66620 mRNA. Translation: AAC52794.1. Sequence problems.
BC026783 mRNA. Translation: AAH26783.3. Different initiation.
BC059921 mRNA. No translation available.
AK075611 mRNA. Translation: BAC35856.1.
CCDSiCCDS37204.1. [Q61466-1]
PIRiA30222.
RefSeqiNP_114030.2. NM_031842.2. [Q61466-1]
UniGeneiMm.273756.

3D structure databases

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

Protein-protein interaction databases

BioGridi219977. 15 interactors.
DIPiDIP-33019N.
IntActiQ61466. 9 interactors.
MINTiMINT-4134901.
STRINGi10090.ENSMUSP00000023759.

PTM databases

iPTMnetiQ61466.
PhosphoSitePlusiQ61466.

Proteomic databases

PaxDbiQ61466.
PeptideAtlasiQ61466.
PRIDEiQ61466.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000023759; ENSMUSP00000023759; ENSMUSG00000023018. [Q61466-1]
GeneIDi83797.
KEGGimmu:83797.
UCSCiuc007xqb.1. mouse. [Q61466-1]

Organism-specific databases

CTDi6602.
MGIiMGI:1933623. Smarcd1.

Phylogenomic databases

eggNOGiKOG2570. Eukaryota.
COG5531. LUCA.
GeneTreeiENSGT00390000017809.
HOGENOMiHOG000240746.
HOVERGENiHBG054046.
InParanoidiQ61466.
KOiK11650.
OMAiQQPAFQS.
OrthoDBiEOG091G06WW.
PhylomeDBiQ61466.
TreeFamiTF106486.

Enzyme and pathway databases

ReactomeiR-MMU-3214858. RMTs methylate histone arginines.

Miscellaneous databases

EvolutionaryTraceiQ61466.
PROiQ61466.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000023018.
GenevisibleiQ61466. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: Q61466
Secondary accession number(s): P70384, Q8R0I7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 26, 2009
Last modified: November 2, 2016
This is version 132 of the entry and version 3 of the sequence. [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

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.