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Q92784 (DPF3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length378 AA.
Sequence statusComplete.
Protein existenceEvidence 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.

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 378378Zinc finger protein DPF3
PRO_0000168154

Regions

Zinc finger198 – 22124C2H2-type
Zinc finger259 – 31961PHD-type 1
Zinc finger316 – 36651PHD-type 2

Natural variations

Alternative sequence1 – 1111MATVIHNPLKA → MFYGRINGRNFAASSLPVAF AATPLMLFLPNPQLICSFPI SSRNHITGLMPPGKLKLENL FHMCTR in isoform 3.
VSP_035882
Alternative sequence177 – 378202RGSAG…FGCQA → RCPLPSLHCFLPSLCRDRC in isoform 4.
VSP_035883
Alternative sequence291 – 37888GHPTC…FGCQA → AHLGGEGRKEKEAAAAARTT EDLFGSTSESDTSTFHGFDE DDLEEPRSCRGRRSGRGSPT ADKKGSC in isoform 2 and isoform 3.
VSP_035884
Natural variant1771R → H. Ref.4
Corresponds to variant rs17855717 [ dbSNP | Ensembl ].
VAR_047771
Isoform 2:
Natural variant3261H → R in dbSNP: rs17855716.

Experimental info

Mutagenesis3581W → E: Abolishes binding to acetylated histones H3 and H4. Ref.1
Mutagenesis3601C → R: Abolishes binding to acetylated histones H3 and H4; when associated with R-363. Ref.1
Mutagenesis3631C → R: Abolishes binding to acetylated histones H3 and H4; when associated with R-360. Ref.1
Sequence conflict121L → V in AAC50686. Ref.5
Sequence conflict241C → S in AAC50686. Ref.5
Sequence conflict321C → S in BAB14838. Ref.2
Sequence conflict1701N → D in BAB14838. Ref.2
Sequence conflict2071Y → H in BAC86753. Ref.2
Sequence conflict2161H → Y in BAC86753. Ref.2

Secondary structure

............................ 378
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (DPF3b) [UniParc].

Last modified November 25, 2008. Version 3.
Checksum: 7E6A6FD07A0E4668

FASTA37843,084
        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 

« Hide

Isoform 2 (DPF3a) [UniParc].

Checksum: 50914AC52A9AD3FB
Show »

FASTA35740,244
Isoform 3 [UniParc].

Checksum: BB778F504DF34AD9
Show »

FASTA41246,401
Isoform 4 [UniParc].

Checksum: 48875102247B766B
Show »

FASTA19522,667

References

« Hide '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. 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 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. expand/collapse author list , 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, DOMAIN PHD.
+Additional computationally mapped references.

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.
RefSeqNP_001267471.1. NM_001280542.1.
NP_001267473.1. NM_001280544.1.
NP_036206.3. NM_012074.4.
UniGeneHs.162868.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2KWJNMR-A261-372[»]
2KWKNMR-A261-372[»]
2KWNNMR-A261-372[»]
2KWONMR-A261-372[»]
ProteinModelPortalQ92784.
SMRQ92784. Positions 192-223, 260-372.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113779. 8 interactions.
DIPDIP-59245N.
STRING9606.ENSP00000381791.

PTM databases

PhosphoSiteQ92784.

Polymorphism databases

DMDM215274167.

Proteomic databases

PaxDbQ92784.
PRIDEQ92784.

Protocols and materials databases

DNASU8110.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000381216; ENSP00000370614; ENSG00000205683. [Q92784-2]
ENST00000541685; ENSP00000441640; ENSG00000205683. [Q92784-2]
ENST00000556509; ENSP00000450518; ENSG00000205683. [Q92784-1]
GeneID8110.
KEGGhsa:8110.
UCSCuc001xnc.2. human. [Q92784-1]
uc010ari.1. human. [Q92784-2]

Organism-specific databases

CTD8110.
GeneCardsGC14M073086.
HGNCHGNC:17427. DPF3.
MIM601672. gene.
neXtProtNX_Q92784.
PharmGKBPA134888535.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG271547.
HOGENOMHOG000217918.
HOVERGENHBG004475.
OMATNMTEAV.
PhylomeDBQ92784.
TreeFamTF318971.

Gene expression databases

ArrayExpressQ92784.
BgeeQ92784.
CleanExHS_DPF3.
GenevestigatorQ92784.

Family and domain databases

Gene3D3.30.40.10. 2 hits.
InterProIPR025750. 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]
PfamPF00628. PHD. 1 hit.
PF14051. Requiem_N. 1 hit.
[Graphical view]
SMARTSM00249. PHD. 2 hits.
SM00184. RING. 2 hits.
SM00355. ZnF_C2H2. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 2 hits.
PROSITEPS01359. 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]
ProtoNetSearch...

Other

EvolutionaryTraceQ92784.
GenomeRNAi8110.
NextBio30759.
PROQ92784.
SOURCESearch...

Entry information

Entry nameDPF3_HUMAN
AccessionPrimary (citable) accession number: Q92784
Secondary accession number(s): A8MSI3 expand/collapse secondary AC list , Q32UJ0, Q6P9E6, Q6ZT41, Q9H7Y5
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 25, 2008
Last modified: April 16, 2014
This is version 106 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

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

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 14

Human chromosome 14: entries, gene names and cross-references to MIM