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Protein

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

Gene

SMARCE1

Organism
Homo sapiens (Human)
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. 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). Required for the coactivation of estrogen responsive promoters by SWI/SNF complexes and the SRC/p160 family of histone acetyltransferases (HATs). Also specifically interacts with the CoREST corepressor resulting in repression of neuronal specific gene promoters in non-neuronal cells.3 PublicationsBy similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi66 – 134HMG boxPROSITE-ProRule annotationAdd BLAST69

GO - Molecular functioni

  • chromatin binding Source: ProtInc
  • DNA binding Source: UniProtKB-KW
  • ligand-dependent nuclear receptor binding Source: BHF-UCL
  • N-acetyltransferase activity Source: UniProtKB
  • protein N-terminus binding Source: UniProtKB
  • RNA binding Source: Ensembl
  • transcription coactivator activity Source: ProtInc

GO - Biological processi

  • ATP-dependent chromatin remodeling Source: UniProtKB
  • chromatin remodeling Source: BHF-UCL
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • neurogenesis Source: Ensembl
  • nucleosome disassembly Source: BHF-UCL
  • regulation of transcription by RNA polymerase II Source: ProtInc

Keywordsi

Molecular functionChromatin regulator, DNA-binding
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
SIGNORiQ969G3

Names & Taxonomyi

Protein namesi
Recommended name:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
Alternative name(s):
BRG1-associated factor 57
Short name:
BAF57
Gene namesi
Name:SMARCE1
Synonyms:BAF57
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

EuPathDBiHostDB:ENSG00000073584.18
HGNCiHGNC:11109 SMARCE1
MIMi603111 gene
neXtProtiNX_Q969G3

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

Involvement in diseasei

Meningioma (MNGMA)2 Publications
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA common neoplasm of the central nervous system derived from arachnoidal cells. The majority of meningiomas are well differentiated vascular tumors which grow slowly and have a low potential to be invasive, although malignant subtypes occur. Most cases are sporadic. Familial occurrence of meningioma is rare.
See also OMIM:607174
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_071873125 – 132EYNESMKA → GLHRFIVL in MNGMA; found in a case of childhood clear cell meningioma; associated with disease susceptibility. 1 Publication8
Coffin-Siris syndrome 5 (CSS5)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported.
See also OMIM:616938
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06821573Y → C in CSS5. 1 PublicationCorresponds to variant dbSNP:rs387906857EnsemblClinVar.1
Natural variantiVAR_07693273Y → S in CSS5. 1 PublicationCorresponds to variant dbSNP:rs387906857EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi6605
GeneReviewsiSMARCE1
MalaCardsiSMARCE1
MIMi607174 phenotype
616938 phenotype
OpenTargetsiENSG00000073584
Orphaneti1465 Coffin-Siris syndrome
263662 Familial multiple meningioma
PharmGKBiPA35959

Polymorphism and mutation databases

BioMutaiSMARCE1
DMDMi61247587

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000485771 – 411SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1Add BLAST411

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki3Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei4Omega-N-methylarginineCombined sources1
Modified residuei40Omega-N-methylarginineCombined sources1
Cross-linki92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources
Cross-linki92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki131Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki146Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki166Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei265PhosphoserineCombined sources1
Cross-linki277Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Post-translational modificationi

Ubiquitinated by TRIP12, leading to its degradation by the proteasome. Ubiquitination is prevented upon interaction between TRIP12 and SMARCC1.1 Publication

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ969G3
MaxQBiQ969G3
PaxDbiQ969G3
PeptideAtlasiQ969G3
PRIDEiQ969G3

PTM databases

iPTMnetiQ969G3
PhosphoSitePlusiQ969G3

Expressioni

Gene expression databases

BgeeiENSG00000073584
CleanExiHS_SMARCE1
ExpressionAtlasiQ969G3 baseline and differential
GenevisibleiQ969G3 HS

Organism-specific databases

HPAiCAB037318
HPA003916

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:12672490, PubMed:22952240, PubMed:26601204). Component of the BAF complex, which includes at least actin (ACTB), ARID1A/BAF250A, ARID1B/BAF250B, SMARCA2/BRM/BAF190B, 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 (PubMed:18765789). 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. 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 (ACTB) (PubMed:22952240, PubMed:26601204). Interacts with BRDT (By similarity). Also binds to the SRC/p160 family of histone acetyltransferases (HATs) composed of NCOA1, NCOA2, and NCOA3. Interacts with RCOR1/CoREST, NR3C1 and ZMIM2/ZIMP7 (PubMed:12192000, PubMed:12917342, PubMed:16051670).3 PublicationsBy similarity4 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • ligand-dependent nuclear receptor binding Source: BHF-UCL
  • protein N-terminus binding Source: UniProtKB

Protein-protein interaction databases

BioGridi112489, 127 interactors
CORUMiQ969G3
DIPiDIP-27614N
DIP-33041N
IntActiQ969G3, 97 interactors
MINTiQ969G3
STRINGi9606.ENSP00000323967

Structurei

3D structure databases

ProteinModelPortaliQ969G3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili220 – 319Sequence analysisAdd BLAST100

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi5 – 65Pro-richAdd BLAST61
Compositional biasi320 – 411Glu-richAdd BLAST92

Domaini

The HMG domain is essential for CD4 silencing and CD8 activation; mutation of this domain blocks thymus development.

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG4715 Eukaryota
ENOG410Y9B3 LUCA
GeneTreeiENSGT00390000003628
HOGENOMiHOG000230965
HOVERGENiHBG054558
InParanoidiQ969G3
KOiK11651
OMAiCCMKVEV
OrthoDBiEOG091G0ER1
PhylomeDBiQ969G3
TreeFamiTF321146

Family and domain databases

Gene3Di1.10.30.10, 1 hit
InterProiView protein in InterPro
IPR030089 BAF57
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf
PANTHERiPTHR13711:SF206 PTHR13711:SF206, 1 hit
PfamiView protein in Pfam
PF00505 HMG_box, 1 hit
SMARTiView protein in SMART
SM00398 HMG, 1 hit
SUPFAMiSSF47095 SSF47095, 1 hit
PROSITEiView protein in PROSITE
PS50118 HMG_BOX_2, 1 hit

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q969G3-1) [UniParc]FASTAAdd to basket
Also known as: BAF57

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
MSKRPSYAPP PTPAPATQMP STPGFVGYNP YSHLAYNNYR LGGNPGTNSR
60 70 80 90 100
VTASSGITIP KPPKPPDKPL MPYMRYSRKV WDQVKASNPD LKLWEIGKII
110 120 130 140 150
GGMWRDLTDE EKQEYLNEYE AEKIEYNESM KAYHNSPAYL AYINAKSRAE
160 170 180 190 200
AALEEESRQR QSRMEKGEPY MSIQPAEDPD DYDDGFSMKH TATARFQRNH
210 220 230 240 250
RLISEILSES VVPDVRSVVT TARMQVLKRQ VQSLMVHQRK LEAELLQIEE
260 270 280 290 300
RHQEKKRKFL ESTDSFNNEL KRLCGLKVEV DMEKIAAEIA QAEEQARKRQ
310 320 330 340 350
EEREKEAAEQ AERSQSSIVP EEEQAANKGE EKKDDENIPM ETEETHLEET
360 370 380 390 400
TESQQNGEEG TSTPEDKESG QEGVDSMAEE GTSDSNTGSE SNSATVEEPP
410
TDPIPEDEKK E
Length:411
Mass (Da):46,649
Last modified:October 25, 2004 - v2
Checksum:i6F1C1B7917BAD506
GO
Isoform 2 (identifier: Q969G3-2) [UniParc]FASTAAdd to basket
Also known as: BAF57v

The sequence of this isoform differs from the canonical sequence as follows:
     344-363: ETHLEETTESQQNGEEGTST → KNCQLCPRKTLTSRYTDFPD
     364-411: Missing.

Show »
Length:363
Mass (Da):41,780
Checksum:iCAADA4121B64578D
GO
Isoform 3 (identifier: Q969G3-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-70: Missing.

Show »
Length:341
Mass (Da):39,260
Checksum:i8E5D2873CC92A598
GO
Isoform 4 (identifier: Q969G3-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     17-51: Missing.

Show »
Length:376
Mass (Da):42,836
Checksum:i945FCF2B107F5429
GO
Isoform 5 (identifier: Q969G3-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     17-51: Missing.
     344-411: ETHLEETTES...DPIPEDEKKE → KNCQLCPRKTLTSRYTDFPD

Show »
Length:328
Mass (Da):37,967
Checksum:iB87AE458E82C27A5
GO
Isoform 6 (identifier: Q969G3-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-70: Missing.
     344-411: ETHLEETTES...DPIPEDEKKE → KNCQLCPRKTLTSRYTDFPD

Show »
Length:293
Mass (Da):34,390
Checksum:iFD0A8E38AD0ADC91
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti46G → S in AAP35840 (Ref. 3) Curated1
Sequence conflicti46G → S in AAH07082 (PubMed:15489334).Curated1
Sequence conflicti46G → S in AAH11017 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06821573Y → C in CSS5. 1 PublicationCorresponds to variant dbSNP:rs387906857EnsemblClinVar.1
Natural variantiVAR_07693273Y → S in CSS5. 1 PublicationCorresponds to variant dbSNP:rs387906857EnsemblClinVar.1
Natural variantiVAR_071873125 – 132EYNESMKA → GLHRFIVL in MNGMA; found in a case of childhood clear cell meningioma; associated with disease susceptibility. 1 Publication8

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0476041 – 70Missing in isoform 3 and isoform 6. 2 PublicationsAdd BLAST70
Alternative sequenceiVSP_04782517 – 51Missing in isoform 4 and isoform 5. 1 PublicationAdd BLAST35
Alternative sequenceiVSP_047826344 – 411ETHLE…DEKKE → KNCQLCPRKTLTSRYTDFPD in isoform 5 and isoform 6. 1 PublicationAdd BLAST68
Alternative sequenceiVSP_011801344 – 363ETHLE…EGTST → KNCQLCPRKTLTSRYTDFPD in isoform 2. 1 PublicationAdd BLAST20
Alternative sequenceiVSP_011802364 – 411Missing in isoform 2. 1 PublicationAdd BLAST48

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF035262 Genomic DNA Translation: AAC04509.1
EU327017 mRNA Translation: ACA81391.1
EU327018 mRNA Translation: ACA81392.1
EU327019 mRNA Translation: ACA81393.1
EU327020 mRNA Translation: ACA81394.1
BT007176 mRNA Translation: AAP35840.1
AK001532 mRNA Translation: BAG50933.1
AK095047 mRNA Translation: BAG52975.1
AK294218 mRNA Translation: BAG57525.1
AC004585 Genomic DNA No translation available.
AC073508 Genomic DNA No translation available.
CH471152 Genomic DNA Translation: EAW60670.1
BC007082 mRNA Translation: AAH07082.1
BC011017 mRNA Translation: AAH11017.1
BC063700 mRNA Translation: AAH63700.1
CCDSiCCDS11370.1 [Q969G3-1]
RefSeqiNP_003070.3, NM_003079.4 [Q969G3-1]
UniGeneiHs.743978

Genome annotation databases

EnsembliENST00000348513; ENSP00000323967; ENSG00000073584 [Q969G3-1]
ENST00000377808; ENSP00000367039; ENSG00000073584 [Q969G3-5]
ENST00000400122; ENSP00000411607; ENSG00000073584 [Q969G3-6]
ENST00000578044; ENSP00000464511; ENSG00000073584 [Q969G3-3]
ENST00000580419; ENSP00000462475; ENSG00000073584 [Q969G3-4]
GeneIDi6605
KEGGihsa:6605
UCSCiuc002hux.4 human [Q969G3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiSMCE1_HUMAN
AccessioniPrimary (citable) accession number: Q969G3
Secondary accession number(s): B3KMC1
, B4DFR4, C0IMW4, C0IMW5, C0IMW7, H7C3F6, O43539
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2004
Last sequence update: October 25, 2004
Last modified: May 23, 2018
This is version 164 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

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