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Q96GM5 (SMRD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
SWI/SNF complex 60 kDa subunit
Gene names
Name:SMARCD1
Synonyms:BAF60A
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length515 AA.
Sequence statusComplete.
Protein existenceEvidence 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. Ref.1 Ref.5 Ref.6 Ref.7

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.4 Ref.5 Ref.6 Ref.7 Ref.8

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.

The sequence AAD23390.1 differs from that shown. Reason: Erroneous initiation.

The sequence AAH09368.3 differs from that shown. Reason: Erroneous initiation.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Nr3c1P065362EBI-358489,EBI-1187143From a different organism.
SMARCA4P515327EBI-358489,EBI-302489
SMARCC1Q929223EBI-358489,EBI-355653

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 515515SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
PRO_0000071983

Regions

Domain291 – 390100SWIB
Region43 – 167125Interaction with ESR1, NR1H4, NR3C1, PGR and SMARCA4
Region168 – 474307Interaction with SMARCC1 and SMARCC2
Region180 – 515336Necessary for GR/NR3C1-mediated remodeling and transcription from chromatin; required for GR/NR3C1 interaction with the BRG1/SMARCA4 complex in vivo
Coiled coil412 – 44029 Potential
Compositional bias124 – 1274Poly-Lys

Amino acid modifications

Modified residue2231N6-acetyllysine By similarity

Natural variations

Alternative sequence423 – 46341Missing in isoform 2.
VSP_004179

Experimental info

Sequence conflict3491S → T in AAC50695. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 26, 2009. Version 2.
Checksum: E683AA1E345DA400

FASTA51558,233
        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 

« Hide

Isoform 2 [UniParc].

Checksum: 2DA7AB84B9A3F933
Show »

FASTA47453,299

References

« Hide '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] [Europe PMC] [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. expand/collapse author list , 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE BAF COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
+Additional computationally mapped references.

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.
RefSeqNP_003067.3. NM_003076.4.
NP_620710.2. NM_139071.2.
UniGeneHs.79335.

3D structure databases

ProteinModelPortalQ96GM5.
SMRQ96GM5. Positions 291-370.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112486. 75 interactions.
DIPDIP-33390N.
IntActQ96GM5. 43 interactions.
MINTMINT-1144212.
STRING9606.ENSP00000378414.

PTM databases

PhosphoSiteQ96GM5.

Polymorphism databases

DMDM238054318.

Proteomic databases

PaxDbQ96GM5.
PRIDEQ96GM5.

Protocols and materials databases

DNASU6602.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000381513; ENSP00000370924; ENSG00000066117. [Q96GM5-2]
ENST00000394963; ENSP00000378414; ENSG00000066117. [Q96GM5-1]
GeneID6602.
KEGGhsa:6602.
UCSCuc001rvx.4. human. [Q96GM5-1]
uc001rvy.4. human. [Q96GM5-2]

Organism-specific databases

CTD6602.
GeneCardsGC12P050478.
HGNCHGNC:11106. SMARCD1.
HPAHPA004101.
MIM601735. gene.
neXtProtNX_Q96GM5.
PharmGKBPA35956.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5531.
HOGENOMHOG000240746.
HOVERGENHBG054046.
InParanoidQ96GM5.
KOK11650.
OMAIFETQRM.
OrthoDBEOG7PZRXG.
PhylomeDBQ96GM5.
TreeFamTF106486.

Gene expression databases

ArrayExpressQ96GM5.
BgeeQ96GM5.
CleanExHS_SMARCD1.
GenevestigatorQ96GM5.

Family and domain databases

Gene3D1.10.245.10. 1 hit.
InterProIPR019835. SWIB_domain.
IPR003121. SWIB_MDM2_domain.
[Graphical view]
PfamPF02201. SWIB. 1 hit.
[Graphical view]
SMARTSM00151. SWIB. 1 hit.
[Graphical view]
SUPFAMSSF47592. SSF47592. 1 hit.
ProtoNetSearch...

Other

ChiTaRSSMARCD1. human.
GeneWikiSMARCD1.
GenomeRNAi6602.
NextBio25683.
PROQ96GM5.
SOURCESearch...

Entry information

Entry nameSMRD1_HUMAN
AccessionPrimary (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: April 16, 2014
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 12

Human chromosome 12: entries, gene names and cross-references to MIM