Q92784 (DPF3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Zinc finger protein DPF3

Alternative name(s):
BRG1-associated factor 45C
Short name=BAF45C
Zinc finger protein cer-d4

Gene names

Name:	DPF3
Synonyms:	BAF45C, CERD4

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	378 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Belongs to 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. Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development. Ref.1
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. Interacts with acetylated histones H3 and H4. 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.1
Subcellular location	Nucleus Probable.
Domain	The PHD-type zinc fingers mediate the binding to acetylated histones. Ref.1 Ref.6
Sequence similarities	Belongs to the requiem/DPF family. Contains 1 C2H2-type zinc finger. Contains 2 PHD-type zinc fingers.
Sequence caution	Isoform 4: The sequence BAB14838.1 differs from that shown. Reason: Frameshift at position 187.

Ontologies

Keywords
Biological process	Neurogenesis Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Activator Chromatin regulator Repressor
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW nervous system development Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nBAF complex Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	zinc ion binding Non-traceable author statement Ref.5. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q92784-1)

Also known as: DPF3b;

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 (identifier: Q92784-2)

Also known as: DPF3a;

The sequence of this isoform differs from the canonical sequence as follows:
     291-378: GHPTCLQFTL...EKASAFGCQA → AHLGGEGRKE...SPTADKKGSC

Note: Lacks PHD-type zinc fingers and does not bind to acetylated histones H3 and H4.

Isoform 3 (identifier: Q92784-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-11: MATVIHNPLKA → MFYGRINGRN...LENLFHMCTR
     291-378: GHPTCLQFTL...EKASAFGCQA → AHLGGEGRKE...SPTADKKGSC

Note: No experimental confirmation available.

Isoform 4 (identifier: Q92784-4)

The sequence of this isoform differs from the canonical sequence as follows:
     177-378: RGSAGGRRRH...EKASAFGCQA → RCPLPSLHCFLPSLCRDRC

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 378

378

Zinc finger protein DPF3

PRO_0000168154

Regions

Zinc finger

198 – 221

24

C2H2-type

Zinc finger

259 – 319

61

PHD-type 1

Zinc finger

316 – 366

51

PHD-type 2

Natural variations

Alternative sequence

1 – 11

11

MATVIHNPLKA → MFYGRINGRNFAASSLPVAF AATPLMLFLPNPQLICSFPI SSRNHITGLMPPGKLKLENL FHMCTR in isoform 3.

VSP_035882

Alternative sequence

177 – 378

202

RGSAG…FGCQA → RCPLPSLHCFLPSLCRDRC in isoform 4.

VSP_035883

Alternative sequence

291 – 378

88

GHPTC…FGCQA → AHLGGEGRKEKEAAAAARTT EDLFGSTSESDTSTFHGFDE DDLEEPRSCRGRRSGRGSPT ADKKGSC in isoform 2 and isoform 3.

VSP_035884

Natural variant

177

1

R → H. Ref.4
Corresponds to variant rs17855717 [ dbSNP | Ensembl ].

VAR_047771

Isoform 2:

Natural variant

326

1

H → R in dbSNP: rs17855716.

Experimental info

Mutagenesis

358

1

W → E: Abolishes binding to acetylated histones H3 and H4. Ref.1

Mutagenesis

360

1

C → R: Abolishes binding to acetylated histones H3 and H4; when associated with R-363. Ref.1

Mutagenesis

363

1

C → R: Abolishes binding to acetylated histones H3 and H4; when associated with R-360. Ref.1

Sequence conflict

12

1

L → V in AAC50686. Ref.5

Sequence conflict

24

1

C → S in AAC50686. Ref.5

Sequence conflict

32

1

C → S in BAB14838. Ref.2

Sequence conflict

170

1

N → D in BAB14838. Ref.2

Sequence conflict

207

1

Y → H in BAC86753. Ref.2

Sequence conflict

216

1

H → Y in BAC86753. Ref.2

Secondary structure

1

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378

Helix Strand Turn

Details...

Beta strand

263 – 265

3

Turn

273 – 275

3

Beta strand

285 – 287

3

Turn

293 – 297

5

Helix

300 – 308

9

Helix

314 – 316

3

Turn

320 – 322

3

Turn

326 – 330

5

Beta strand

331 – 333

3

Beta strand

335 – 337

3

Beta strand

340 – 342

3

Turn

343 – 345

3

Beta strand

346 – 348

3

Beta strand

355 – 357

3

Helix

361 – 369

9

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (DPF3b) [UniParc]. Last modified November 25, 2008. Version 3. Checksum: 7E6A6FD07A0E4668	FASTA	378	43,084
	10 20 30 40 50 60 MATVIHNPLK ALGDQFYKEA IEHCRSYNSR LCAERSVRLP FLDSQTGVAQ NNCYIWMEKR 70 80 90 100 110 120 HRGPGLAPGQ LYTYPARCWR KKRRLHPPED PKLRLLEIKP EVELPLKKDG FTSESTTLEA 130 140 150 160 170 180 LLRGEGVEKK VDAREEESIQ EIQRVLENDE NVEEGNEEED LEEDIPKRKN RTRGRARGSA 190 200 210 220 230 240 GGRRRHDAAS QEDHDKPYVC DICGKRYKNR PGLSYHYAHT HLASEEGDEA QDQETRSPPN 250 260 270 280 290 300 HRNENHRPQK GPDGTVIPNN YCDFCLGGSN MNKKSGRPEE LVSCADCGRS GHPTCLQFTL 310 320 330 340 350 360 NMTEAVKTYK WQCIECKSCI LCGTSENDDQ LLFCDDCDRG YHMYCLNPPV AEPPEGSWSC 370 HLCWELLKEK ASAFGCQA
	Isoform 2 (DPF3a) [UniParc]. Checksum: 50914AC52A9AD3FB	FASTA	357	40,244
	10 20 30 40 50 60 MATVIHNPLK ALGDQFYKEA IEHCRSYNSR LCAERSVRLP FLDSQTGVAQ NNCYIWMEKR 70 80 90 100 110 120 HRGPGLAPGQ LYTYPARCWR KKRRLHPPED PKLRLLEIKP EVELPLKKDG FTSESTTLEA 130 140 150 160 170 180 LLRGEGVEKK VDAREEESIQ EIQRVLENDE NVEEGNEEED LEEDIPKRKN RTRGRARGSA 190 200 210 220 230 240 GGRRRHDAAS QEDHDKPYVC DICGKRYKNR PGLSYHYAHT HLASEEGDEA QDQETRSPPN 250 260 270 280 290 300 HRNENHRPQK GPDGTVIPNN YCDFCLGGSN MNKKSGRPEE LVSCADCGRS AHLGGEGRKE 310 320 330 340 350 KEAAAAARTT EDLFGSTSES DTSTFHGFDE DDLEEPRSCR GRRSGRGSPT ADKKGSC
	Isoform 3 [UniParc]. Checksum: BB778F504DF34AD9	FASTA	412	46,401
	10 20 30 40 50 60 MFYGRINGRN FAASSLPVAF AATPLMLFLP NPQLICSFPI SSRNHITGLM PPGKLKLENL 70 80 90 100 110 120 FHMCTRLGDQ FYKEAIEHCR SYNSRLCAER SVRLPFLDSQ TGVAQNNCYI WMEKRHRGPG 130 140 150 160 170 180 LAPGQLYTYP ARCWRKKRRL HPPEDPKLRL LEIKPEVELP LKKDGFTSES TTLEALLRGE 190 200 210 220 230 240 GVEKKVDARE EESIQEIQRV LENDENVEEG NEEEDLEEDI PKRKNRTRGR ARGSAGGRRR 250 260 270 280 290 300 HDAASQEDHD KPYVCDICGK RYKNRPGLSY HYAHTHLASE EGDEAQDQET RSPPNHRNEN 310 320 330 340 350 360 HRPQKGPDGT VIPNNYCDFC LGGSNMNKKS GRPEELVSCA DCGRSAHLGG EGRKEKEAAA 370 380 390 400 410 AARTTEDLFG STSESDTSTF HGFDEDDLEE PRSCRGRRSG RGSPTADKKG SC
	Isoform 4 [UniParc]. Checksum: 48875102247B766B	FASTA	195	22,667
	10 20 30 40 50 60 MATVIHNPLK ALGDQFYKEA IEHCRSYNSR LCAERSVRLP FLDSQTGVAQ NNCYIWMEKR 70 80 90 100 110 120 HRGPGLAPGQ LYTYPARCWR KKRRLHPPED PKLRLLEIKP EVELPLKKDG FTSESTTLEA 130 140 150 160 170 180 LLRGEGVEKK VDAREEESIQ EIQRVLENDE NVEEGNEEED LEEDIPKRKN RTRGRARCPL 190 PSLHCFLPSL CRDRC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), FUNCTION, IDENTIFICATION IN THE BAF COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY, DOMAIN, INTERACTION WITH HISTONES, MUTAGENESIS OF TRP-358; CYS-360 AND CYS-363. Tissue: Heart.
[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. , 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 3 AND 4). Tissue: Brain and Embryo.
[3]	"The DNA sequence and analysis of human chromosome 14." Heilig R., Eckenberg R., Petit J.-L., Fonknechten N., Da Silva C., Cattolico L., Levy M., Barbe V., De Berardinis V., Ureta-Vidal A., Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S., Sun H., Du H. , Pepin K., Artiguenave F., Robert C., Cruaud C., Bruels T., Jaillon O., Friedlander L., Samson G., Brottier P., Cure S., Segurens B., Aniere F., Samain S., Crespeau H., Abbasi N., Aiach N., Boscus D., Dickhoff R., Dors M., Dubois I., Friedman C., Gouyvenoux M., James R., Madan A., Mairey-Estrada B., Mangenot S., Martins N., Menard M., Oztas S., Ratcliffe A., Shaffer T., Trask B., Vacherie B., Bellemere C., Belser C., Besnard-Gonnet M., Bartol-Mavel D., Boutard M., Briez-Silla S., Combette S., Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C., Muselet D., Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P., Trybou A., Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M., Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V., Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L., Verdier J., Verdier-Discala C., Hillier L.W., Fulton L., McPherson J., Matsuda F., Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W., Quetier F., Waterston R., Hood L., Weissenbach J. Nature 421:601-607(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"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 2), VARIANT HIS-177. Tissue: Brain.
[5]	"The d4 gene family in the human genome." Chestkov A.V., Baka I.D., Kost M.V., Georgiev G.P., Buchman V.L. Genomics 36:174-177(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-64.
[6]	"Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b." Zeng L., Zhang Q., Li S., Plotnikov A.N., Walsh M.J., Zhou M.M. Nature 466:258-262(2010) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 261-372, PHD DOMAIN.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY803021 mRNA. Translation: AAX20019.1.
AK024141 mRNA. Translation: BAB14838.1. Frameshift.
AK126933 mRNA. Translation: BAC86753.1.
AC004828 Genomic DNA. No translation available.
AC006360 Genomic DNA. No translation available.
AL392024 Genomic DNA. No translation available.
BC060801 mRNA. Translation: AAH60801.1.
U43919 Genomic DNA. Translation: AAC50686.1.

IPI

IPI00425378.
IPI00915028.
IPI00915029.
IPI01012933.

RefSeq

NP_036206.3. NM_012074.3.

UniGene

Hs.162868.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2KWJ	NMR	-	A	261-372	[»]
2KWK	NMR	-	A	261-372	[»]
2KWN	NMR	-	A	261-372	[»]
2KWO	NMR	-	A	261-372	[»]

ProteinModelPortal

Q92784.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-59245N.

STRING

9606.ENSP00000381791.

PTM databases

PhosphoSite

Q92784.

Polymorphism databases

DMDM

215274167.

Proteomic databases

PaxDb

Q92784.

PRIDE

Q92784.

Protocols and materials databases

DNASU

8110.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000381216; ENSP00000370614; ENSG00000205683.
ENST00000541685; ENSP00000441640; ENSG00000205683.
ENST00000556509; ENSP00000450518; ENSG00000205683.

GeneID

8110.

KEGG

hsa:8110.

UCSC

uc001xnc.2. human.
uc010ari.1. human.

Organism-specific databases

CTD

8110.

GeneCards

GC14M073086.

HGNC

HGNC:17427. DPF3.

MIM

601672. gene.

neXtProt

NX_Q92784.

PharmGKB

PA134888535.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG271547.

HOGENOM

HOG000217918.

HOVERGEN

HBG004475.

OMA

TNMTEAV.

OrthoDB

EOG4T4CX1.

Gene expression databases

ArrayExpress

Q92784.

Bgee

Q92784.

CleanEx

HS_DPF3.

Genevestigator

Q92784.

GermOnline

ENSG00000205683. Homo sapiens.

Family and domain databases

Gene3D

3.30.40.10. 2 hits.

InterPro

IPR025750. Requiem/DPF_N_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]

Pfam

PF00628. PHD. 1 hit.
PF14051. Requiem_N. 1 hit.
[Graphical view]

SMART

SM00249. PHD. 2 hits.
SM00184. RING. 2 hits.
SM00355. ZnF_C2H2. 1 hit.
[Graphical view]

SUPFAM

SSF57903. FYVE_PHD_ZnF. 2 hits.

PROSITE

PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 2 hits.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
PS50157. ZINC_FINGER_C2H2_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q92784.

GenomeRNAi

8110.

NextBio

30759.

SOURCE

Search...

Entry information

Entry name

DPF3_HUMAN

Accession

Primary (citable) accession number: Q92784
Secondary accession number(s): A8MSI3 , Q32UJ0, Q6P9E6, Q6ZT41, Q9H7Y5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 25, 2008
Last modified:	May 1, 2013
This is version 97 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

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.