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Q92925 (SMRD2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 115. 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 2
Alternative name(s):
60 kDa BRG-1/Brm-associated factor subunit B
BRG1-associated factor 60B
Short name=BAF60B
Gene names
Name:SMARCD2
Synonyms:BAF60B
ORF Names:PRO2451
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length531 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).

Subunit structure

Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1, 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. May interact with SMARCA4, the catalytic subunit of the SWI/SNF related nucleosome-remodeling complexes BRG1(I) and BRG1(II). The precise distribution of the related SMARCD1, SMARCD2 and SMARCD3 proteins among these and other SWI/SNF nucleosome-remodeling complexes is not fully known. Interacts with UNKL. Ref.12 Ref.13

Subcellular location

Nucleus.

Tissue specificity

Isoform 2 is expressed in the pancreas. Ref.1

Post-translational modification

Ubiquitinated through a signaling process involving RAC1 and the RING finger protein UNKL. Ref.12

Sequence similarities

Belongs to the SMARCD family.

Contains 1 SWIB domain.

Sequence caution

The sequence AAC50696.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAF20280.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

UNKLQ9H9P52EBI-358441,EBI-7797561

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q92925-1)

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.
Note: No experimental confirmation available.
Isoform 2 (identifier: Q92925-2)

The sequence of this isoform differs from the canonical sequence as follows:
     48-68: Missing.
     86-123: GLQVGPPAGS...PFRKRLLVPQ → RLAGGTPCWL...SIPKTPACAP
Note: Produced by aberrant splicing sites.
Isoform 3 (identifier: Q92925-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-71: MSGRGAGGFP...MGPAGPAAQY → MGRRVGVEVTPRWAPQKCQGARP

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 531531SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2
PRO_0000071985

Regions

Domain307 – 38276SWIB
Compositional bias10 – 129120Pro-rich

Amino acid modifications

Modified residue2171Phosphothreonine Ref.7 Ref.8 Ref.14 Ref.16

Natural variations

Alternative sequence1 – 7171MSGRG…PAAQY → MGRRVGVEVTPRWAPQKCQG ARP in isoform 3.
VSP_040530
Alternative sequence48 – 6821Missing in isoform 2.
VSP_040531
Alternative sequence86 – 12338GLQVG…LLVPQ → RLAGGTPCWLPIWCSSSAST WHPTHHDGSIPKTPACAP in isoform 2.
VSP_040532

Experimental info

Sequence conflict111L → V in AAC50696. Ref.1
Sequence conflict281P → Q in AAI42964. Ref.5
Sequence conflict2691N → G in AAC50696. Ref.1
Sequence conflict275 – 2762HR → YW in AAC50696. Ref.1
Sequence conflict3321M → T in AAI42964. Ref.5
Sequence conflict3691R → S in AAI42964. Ref.5
Sequence conflict3721E → K in AAI42964. Ref.5
Sequence conflict4861I → T in AAC50696. Ref.1

Sequences

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

Last modified February 8, 2011. Version 3.
Checksum: 8C92168AE7782814

FASTA53158,921
        10         20         30         40         50         60 
MSGRGAGGFP LPPLSPGGGA VAAALGAPPP PAGPGMLPGP ALRGPGPAGG VGGPGAAAFR 

        70         80         90        100        110        120 
PMGPAGPAAQ YQRPGMSPGN RMPMAGLQVG PPAGSPFGAA APLRPGMPPT MMDPFRKRLL 

       130        140        150        160        170        180 
VPQAQPPMPA QRRGLKRRKM ADKVLPQRIR ELVPESQAYM DLLAFERKLD QTIARKRMEI 

       190        200        210        220        230        240 
QEAIKKPLTQ KRKLRIYISN TFSPSKAEGD SAGTAGTPGG TPAGDKVASW ELRVEGKLLD 

       250        260        270        280        290        300 
DPSKQKRKFS SFFKSLVIEL DKELYGPDNH LVEWHRMPTT QETDGFQVKR PGDLNVKCTL 

       310        320        330        340        350        360 
LLMLDHQPPQ YKLDPRLARL LGVHTQTRAA IMQALWLYIK HNQLQDGHER EYINCNRYFR 

       370        380        390        400        410        420 
QIFSCGRLRF SEIPMKLAGL LQHPDPIVIN HVISVDPNDQ KKTACYDIDV EVDDPLKAQM 

       430        440        450        460        470        480 
SNFLASTTNQ QEIASLDVKI HETIESINQL KTQRDFMLSF STDPQDFIQE WLRSQRRDLK 

       490        500        510        520        530 
IITDVIGNPE EERRAAFYHQ PWAQEAVGRH IFAKVQQRRQ ELEQVLGIRL T 

« Hide

Isoform 2 [UniParc].

Checksum: B44CF9CA48DB6065
Show »

FASTA51057,244
Isoform 3 [UniParc].

Checksum: F81547E527C34871
Show »

FASTA48355,239

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] (ISOFORM 2), TISSUE SPECIFICITY.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
Tissue: Small intestine and Trachea.
[3]"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. expand/collapse author list , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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: Uterus.
[6]"Functional prediction of the coding sequences of 14 new genes deduced by analysis of cDNA clones from human fetal liver."
Zhang C., Yu Y., Zhang S., Ouyang S., Luo L., Wei H., Zhou G., Liu M., He F.
Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 450-531.
Tissue: Fetal liver.
[7]"A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-217, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[8]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-217, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[11]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt."
Lores P., Visvikis O., Luna R., Lemichez E., Gacon G.
FEBS J. 277:1453-1464(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH UNKL, UBIQUITINATION.
[13]"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.
[14]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-217, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[15]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-217, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U66618 mRNA. Translation: AAC50696.1. Different initiation.
AK300939 mRNA. Translation: BAG62568.1.
AK303951 mRNA. Translation: BAG64878.1.
AC015651 Genomic DNA. No translation available.
CH471109 Genomic DNA. Translation: EAW94267.1.
BC018953 mRNA. Translation: AAH18953.2.
BC142963 mRNA. Translation: AAI42964.1.
AF113019 mRNA. Translation: AAF20280.1. Different initiation.
CCDSCCDS45756.1. [Q92925-1]
RefSeqNP_001091896.1. NM_001098426.1. [Q92925-1]
UniGeneHs.250581.

3D structure databases

ProteinModelPortalQ92925.
SMRQ92925. Positions 307-386.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112487. 27 interactions.
DIPDIP-31182N.
IntActQ92925. 7 interactions.
MINTMINT-1138034.
STRING9606.ENSP00000392617.

PTM databases

PhosphoSiteQ92925.

Polymorphism databases

DMDM322510105.

Proteomic databases

MaxQBQ92925.
PaxDbQ92925.
PRIDEQ92925.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000323347; ENSP00000318451; ENSG00000108604. [Q92925-3]
ENST00000448276; ENSP00000392617; ENSG00000108604. [Q92925-1]
GeneID6603.
KEGGhsa:6603.
UCSCuc010dea.1. human. [Q92925-1]
uc010wpt.1. human. [Q92925-3]

Organism-specific databases

CTD6603.
GeneCardsGC17M061909.
H-InvDBHIX0014075.
HGNCHGNC:11107. SMARCD2.
HPAHPA051173.
MIM601736. gene.
neXtProtNX_Q92925.
PharmGKBPA35957.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5531.
HOVERGENHBG054046.
KOK11650.
OMAMRFSEIP.
OrthoDBEOG7PZRXG.
PhylomeDBQ92925.
TreeFamTF106486.

Gene expression databases

ArrayExpressQ92925.
BgeeQ92925.
CleanExHS_SMARCD2.
GenevestigatorQ92925.

Family and domain databases

Gene3D1.10.245.10. 1 hit.
InterProIPR003121. SWIB_MDM2_domain.
[Graphical view]
PfamPF02201. SWIB. 1 hit.
[Graphical view]
SUPFAMSSF47592. SSF47592. 1 hit.
ProtoNetSearch...

Other

ChiTaRSSMARCD2. human.
GeneWikiSMARCD2.
GenomeRNAi6603.
NextBio25689.
PROQ92925.
SOURCESearch...

Entry information

Entry nameSMRD2_HUMAN
AccessionPrimary (citable) accession number: Q92925
Secondary accession number(s): A5PLL5 expand/collapse secondary AC list , A6NNQ7, B4DV56, B4E1R6, Q7L2I6, Q9UHZ1
Entry history
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: February 8, 2011
Last modified: July 9, 2014
This is version 115 of the entry and version 3 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 17

Human chromosome 17: entries, gene names and cross-references to MIM