Reviewed, UniProtKB/Swiss-Prot Q96GM5 (SMRD1_HUMAN)

Names and origin

Protein names

Recommended name:
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Alternative name(s):
    SWI/SNF complex 60 kDa subunit
    60 kDa BRG-1/Brm-associated factor subunit A
    BRG1-associated factor 60A
      Short name=BAF60A

Gene names

Name:	SMARCD1
Synonyms:	BAF60A

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	515 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 the 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. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.
Subunit structure	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. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. 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. Ref.6 Ref.7 Ref.4
Subcellular location	Nucleus Probable Ref.1.
Tissue specificity	Expressed in all tissues tested, including brain, heart, kidney, liver, lung, muscle, pancreas and placenta. Ref.1
Sequence similarities	Belongs to the SMARCD family. Contains 1 SWIB domain.
Sequence caution	The sequence AAC50695.1 differs from that shown. Reason: Frameshift at position 30.

Ontologies

Keywords
Biological process	Neurogenesis
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Coiled coil
Molecular function	Chromatin regulator
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	chromatin-mediated maintenance of transcription Ref.7 Inferred from mutant phenotype. Source: UniProtKB regulation of transcription from RNA polymerase II promoter Ref.1 Traceable author statement. Source: ProtInc
Cellular component	SWI/SNF complex Inferred from direct assay. Source: UniProtKB nucleoplasm Ref.1 Traceable author statement. Source: ProtInc nucleus Inferred from direct assay. Source: HPA
Molecular function	protein complex scaffold Ref.7 Inferred from direct assay. Source: UniProtKB transcription coactivator activity Ref.1 Traceable author statement. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ESR1	P03372	1	EBI-358489,EBI-78473
GRB2	P62993	1	EBI-358489,EBI-401755
NR1H4	Q96RI1	1	EBI-358489,EBI-1250177
Nr3c1	P06536	1	EBI-358489,EBI-1187143	From a different organism.
PGR	P06401	1	EBI-358489,EBI-78539
SMARCA4	P51532	2	EBI-358489,EBI-302489
SMARCC1	Q92922	1	EBI-358489,EBI-355653
SMARCC2	Q8TAQ2	1	EBI-358489,EBI-357418

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 Ref.1 (identifier: Q96GM5-1)

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.

Isoform 2 Ref.1 (identifier: Q96GM5-2)

The sequence of this isoform differs from the canonical sequence as follows:
     423-463: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 515	515	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1		PRO_0000071983
Regions
	Domain	291 – 390	100	SWIB
	Region	43 – 167	125	Interaction with ESR1, NR1H4, NR3C1, PGR and SMARCA4
	Region	168 – 474	307	Interaction with SMARCC1 and SMARCC2
	Region	180 – 515	336	Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin; required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo
	Coiled coil	412 – 440	29	Potential
	Compositional bias	124 – 127	4	Poly-Lys
Natural variations
	Alternative sequence	423 – 463	41	Missing in isoform 2.		VSP_004179
Experimental info
	Sequence conflict	349	1	S → T in AAC50695. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 26, 2009. Version 2. Checksum: E683AA1E345DA400	FASTA	515	58,233
	10 20 30 40 50 60 MAARAGFQSV APSGGAGASG GAGAAAALGP GGTPGPPVRM GPAPGQGLYR SPMPGAAYPR 70 80 90 100 110 120 PGMLPGSRMT PQGPSMGPPG YGGNPSVRPG LAQSGMDQSR KRPAPQQIQQ VQQQAVQNRN 130 140 150 160 170 180 HNAKKKKMAD KILPQRIREL VPESQAYMDL LAFERKLDQT IMRKRLDIQE ALKRPIKQKR 190 200 210 220 230 240 KLRIFISNTF NPAKSDAEDG EGTVASWELR VEGRLLEDSA LSKYDATKQK RKFSSFFKSL 250 260 270 280 290 300 VIELDKDLYG PDNHLVEWHR TATTQETDGF QVKRPGDVNV RCTVLLMLDY QPPQFKLDPR 310 320 330 340 350 360 LARLLGIHTQ TRPVIIQALW QYIKTHKLQD PHEREFVICD KYLQQIFESQ RMKFSEIPQR 370 380 390 400 410 420 LHALLMPPEP IIINHVISVD PNDQKKTACY DIDVEVDDTL KTQMNSFLLS TASQQEIATL 430 440 450 460 470 480 DNKIHETIET INQLKTQREF MLSFARDPQG FINDWLQSQC RDLKTMTDVV GNPEEERRAE 490 500 510 FYFQPWAQEA VCRYFYSKVQ QRRQELEQAL GIRNT
	Isoform 2. Checksum: 2DA7AB84B9A3F933	FASTA	474	53,299
	10 20 30 40 50 60 MAARAGFQSV APSGGAGASG GAGAAAALGP GGTPGPPVRM GPAPGQGLYR SPMPGAAYPR 70 80 90 100 110 120 PGMLPGSRMT PQGPSMGPPG YGGNPSVRPG LAQSGMDQSR KRPAPQQIQQ VQQQAVQNRN 130 140 150 160 170 180 HNAKKKKMAD KILPQRIREL VPESQAYMDL LAFERKLDQT IMRKRLDIQE ALKRPIKQKR 190 200 210 220 230 240 KLRIFISNTF NPAKSDAEDG EGTVASWELR VEGRLLEDSA LSKYDATKQK RKFSSFFKSL 250 260 270 280 290 300 VIELDKDLYG PDNHLVEWHR TATTQETDGF QVKRPGDVNV RCTVLLMLDY QPPQFKLDPR 310 320 330 340 350 360 LARLLGIHTQ TRPVIIQALW QYIKTHKLQD PHEREFVICD KYLQQIFESQ RMKFSEIPQR 370 380 390 400 410 420 LHALLMPPEP IIINHVISVD PNDQKKTACY DIDVEVDDTL KTQMNSFLLS TASQQEIATL 430 440 450 460 470 DNKTMTDVVG NPEEERRAEF YFQPWAQEAV CRYFYSKVQQ RRQELEQALG IRNT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Diversity and specialization of mammalian SWI/SNF complexes." Wang W., Xue Y., Zhou S., Kuo A., Cairns B.R., Crabtree G.R. Genes Dev. 10:2117-2130(1996) [PubMed: 8804307] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY. Tissue: Peripheral blood.
[2]	"The finished DNA sequence of human chromosome 12." Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R. , Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Montgomery K.T., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Lovering R.C., Wheeler D.A., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clerc-Blankenburg K.P., Davis C., Delgado O., Dinh H.H., Draper H., Gonzalez-Garay M.L., Havlak P., Jackson L.R., Jacob L.S., Kelly S.H., Li L., Li Z., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Pasternak S., Perez L.M., Plopper F.J.H., Santibanez J., Shen H., Tabor P.E., Verduzco D., Waldron L., Wang Q., Williams G.A., Zhang J., Zhou J., Allen C.C., Amin A.G., Anyalebechi V., Bailey M., Barbaria J.A., Bimage K.E., Bryant N.P., Burch P.E., Burkett C.E., Burrell K.L., Calderon E., Cardenas V., Carter K., Casias K., Cavazos I., Cavazos S.R., Ceasar H., Chacko J., Chan S.N., Chavez D., Christopoulos C., Chu J., Cockrell R., Cox C.D., Dang M., Dathorne S.R., David R., Davis C.M., Davy-Carroll L., Deshazo D.R., Donlin J.E., D'Souza L., Eaves K.A., Egan A., Emery-Cohen A.J., Escotto M., Flagg N., Forbes L.D., Gabisi A.M., Garza M., Hamilton C., Henderson N., Hernandez O., Hines S., Hogues M.E., Huang M., Idlebird D.G., Johnson R., Jolivet A., Jones S., Kagan R., King L.M., Leal B., Lebow H., Lee S., LeVan J.M., Lewis L.C., London P., Lorensuhewa L.M., Loulseged H., Lovett D.A., Lucier A., Lucier R.L., Ma J., Madu R.C., Mapua P., Martindale A.D., Martinez E., Massey E., Mawhiney S., Meador M.G., Mendez S., Mercado C., Mercado I.C., Merritt C.E., Miner Z.L., Minja E., Mitchell T., Mohabbat F., Mohabbat K., Montgomery B., Moore N., Morris S., Munidasa M., Ngo R.N., Nguyen N.B., Nickerson E., Nwaokelemeh O.O., Nwokenkwo S., Obregon M., Oguh M., Oragunye N., Oviedo R.J., Parish B.J., Parker D.N., Parrish J., Parks K.L., Paul H.A., Payton B.A., Perez A., Perrin W., Pickens A., Primus E.L., Pu L.-L., Puazo M., Quiles M.M., Quiroz J.B., Rabata D., Reeves K., Ruiz S.J., Shao H., Sisson I., Sonaike T., Sorelle R.P., Sutton A.E., Svatek A.F., Svetz L.A., Tamerisa K.S., Taylor T.R., Teague B., Thomas N., Thorn R.D., Trejos Z.Y., Trevino B.K., Ukegbu O.N., Urban J.B., Vasquez L.I., Vera V.A., Villasana D.M., Wang L., Ward-Moore S., Warren J.T., Wei X., White F., Williamson A.L., Wleczyk R., Wooden H.S., Wooden S.H., Yen J., Yoon L., Yoon V., Zorrilla S.E., Nelson D., Kucherlapati R., Weinstock G., Gibbs R.A. Nature 440:346-351(2006) [PubMed: 16541075] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Muscle.
[4]	"Purification and biochemical heterogeneity of the mammalian SWI-SNF complex." Wang W., Cote J., Xue Y., Zhou S., Khavari P.A., Biggar S.R., Muchardt C., Kalpana G.V., Goff S.P., Yaniv M., Workman J.L., Crabtree G.R. EMBO J. 15:5370-5382(1996) [PubMed: 8895581] [Abstract] Cited for: SUBUNIT.
[5]	"The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome." Kitagawa H., Fujiki R., Yoshimura K., Mezaki Y., Uematsu Y., Matsui D., Ogawa S., Unno K., Okubo M., Tokita A., Nakagawa T., Ito T., Ishimi Y., Nagasawa H., Matsumoto T., Yanagisawa J., Kato S. Cell 113:905-917(2003) [PubMed: 12837248] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE WINAC COMPLEX, FUNCTION.
[6]	"Use of a modified yeast one-hybrid screen to identify BAF60a interactions with the Vitamin D receptor heterodimer." Koszewski N.J., Henry K.W., Lubert E.J., Gravatte H., Noonan D.J. J. Steroid Biochem. Mol. Biol. 87:223-231(2003) [PubMed: 14698202] [Abstract] Cited for: FUNCTION, INTERACTION WITH THE VITAMIN D RECEPTOR HETERODIMER COMPLEX.
[7]	"BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation." Hsiao P.W., Fryer C.J., Trotter K.W., Wang W., Archer T.K. Mol. Cell. Biol. 23:6210-6220(2003) [PubMed: 12917342] [Abstract] Cited for: FUNCTION, INTERACTION WITH ESR1; NR3C1; NR1H4; PGR; SMARCA4; SMARCC1 AND SMARCC2.
[8]	"Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex." Lange M., Kaynak B., Forster U.B., Toenjes M., Fischer J.J., Grimm C., Schlesinger J., Just S., Dunkel I., Krueger T., Mebus S., Lehrach H., Lurz R., Gobom J., Rottbauer W., Abdelilah-Seyfried S., Sperling S. Genes Dev. 22:2370-2384(2008) [PubMed: 18765789] [Abstract] Cited for: IDENTIFICATION IN THE BAF COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00852816. IPI00853408.
RefSeq	NP_003067.3. NP_620710.2.
UniGene	Hs.79335
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q96GM5. 17 interactions.
STRING	Q96GM5.
Genome annotation databases
Ensembl	ENST00000381513; ENSP00000370924; ENSG00000066117; Homo sapiens. [Genome view] ENST00000394963; ENSP00000378414; ENSG00000066117; Homo sapiens. [Genome view]
GeneID	6602.
KEGG	hsa:6602.
UCSC	uc001rvx.2. human. uc001rvy.2. human.
Organism-specific databases
CTD	6602.
GeneCards	GC12P048768.
H-InvDB	HIX0010621.
HGNC	HGNC:11106. SMARCD1.
HPA	HPA004101.
MIM	601735. gene.
PharmGKB	PA35956.
GenAtlas	Search...
Phylogenomic databases
eggNOG	prNOG11433.
HOGENOM	HBG557568.
HOVERGEN	Q96GM5.
InParanoid	Q96GM5.
OMA	GPAMGPP.
OrthoDB	EOG9D55HF.
Gene expression databases
ArrayExpress	Q96GM5.
Bgee	Q96GM5.
CleanEx	HS_SMARCD1.
Genevestigator	Q96GM5.
Family and domain databases
InterPro	IPR019835. SWIB_domain. IPR003121. SWIB_MDM2_domain. [Graphical view]
Gene3D	G3DSA:1.10.245.10. SWIB_MDM2. 1 hit.
Pfam	PF02201. SWIB. 1 hit. [Graphical view]
SMART	SM00151. SWIB. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	25683.
SOURCE	Search...

Entry information

Entry name

SMRD1_HUMAN

Accession

Primary (citable) accession number: Q96GM5
Secondary accession number(s): A6NN27, Q92924, Q9Y635

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 17, 2003
Last sequence update:	May 26, 2009
Last modified:	February 9, 2010
This is version 75 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.