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Protein

Zinc finger protein DPF3

Gene

DPF3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri198 – 221C2H2-typePROSITE-ProRule annotationAdd BLAST24
Zinc fingeri259 – 319PHD-type 1PROSITE-ProRule annotationAdd BLAST61
Zinc fingeri316 – 366PHD-type 2PROSITE-ProRule annotationAdd BLAST51

GO - Molecular functioni

  • nucleic acid binding Source: InterPro
  • zinc ion binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Repressor

Keywords - Biological processi

Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000011332-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc finger protein DPF3
Alternative name(s):
BRG1-associated factor 45C
Short name:
BAF45C
Zinc finger protein cer-d4
Gene namesi
Name:DPF3
Synonyms:BAF45C, CERD4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:17427. DPF3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi358W → E: Abolishes binding to acetylated histones H3 and H4. 1 Publication1
Mutagenesisi360C → R: Abolishes binding to acetylated histones H3 and H4; when associated with R-363. 1 Publication1
Mutagenesisi363C → R: Abolishes binding to acetylated histones H3 and H4; when associated with R-360. 1 Publication1

Organism-specific databases

DisGeNETi8110.
OpenTargetsiENSG00000205683.
PharmGKBiPA134888535.

Polymorphism and mutation databases

DMDMi215274167.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001681541 – 378Zinc finger protein DPF3Add BLAST378

Proteomic databases

MaxQBiQ92784.
PaxDbiQ92784.
PeptideAtlasiQ92784.
PRIDEiQ92784.

PTM databases

iPTMnetiQ92784.
PhosphoSitePlusiQ92784.

Expressioni

Gene expression databases

BgeeiENSG00000205683.
CleanExiHS_DPF3.
ExpressionAtlasiQ92784. baseline and differential.
GenevisibleiQ92784. HS.

Organism-specific databases

HPAiHPA066790.

Interactioni

Subunit structurei

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).By similarity

Protein-protein interaction databases

BioGridi113779. 26 interactors.
DIPiDIP-59245N.
STRINGi9606.ENSP00000370614.

Structurei

Secondary structure

1378
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni263 – 265Combined sources3
Turni273 – 276Combined sources4
Turni285 – 287Combined sources3
Turni293 – 297Combined sources5
Helixi300 – 306Combined sources7
Turni307 – 310Combined sources4
Turni314 – 316Combined sources3
Turni320 – 322Combined sources3
Beta strandi330 – 333Combined sources4
Turni335 – 337Combined sources3
Beta strandi340 – 342Combined sources3
Turni343 – 345Combined sources3
Beta strandi346 – 348Combined sources3
Beta strandi355 – 357Combined sources3
Helixi361 – 365Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KWJNMR-A261-372[»]
2KWKNMR-A261-372[»]
2KWNNMR-A261-372[»]
2KWONMR-A261-372[»]
5I3LX-ray1.85A/B254-368[»]
ProteinModelPortaliQ92784.
SMRiQ92784.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ92784.

Family & Domainsi

Domaini

The PHD-type zinc fingers mediate the binding to acetylated histones.2 Publications

Sequence similaritiesi

Belongs to the requiem/DPF family.Curated
Contains 1 C2H2-type zinc finger.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri198 – 221C2H2-typePROSITE-ProRule annotationAdd BLAST24
Zinc fingeri259 – 319PHD-type 1PROSITE-ProRule annotationAdd BLAST61
Zinc fingeri316 – 366PHD-type 2PROSITE-ProRule annotationAdd BLAST51

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1244. Eukaryota.
ENOG410YDAG. LUCA.
GeneTreeiENSGT00530000063194.
HOGENOMiHOG000217918.
HOVERGENiHBG004475.
InParanoidiQ92784.
OMAiVAHAACT.
PhylomeDBiQ92784.
TreeFamiTF318971.

Family and domain databases

Gene3Di3.30.160.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR025750. Requiem/DPF_N_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
PF14051. Requiem_N. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
SM00355. ZnF_C2H2. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 2 hits.
PROSITEiPS01359. 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]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q92784-1) [UniParc]FASTAAdd to basket
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.

« Hide

        10         20         30         40         50
MATVIHNPLK ALGDQFYKEA IEHCRSYNSR LCAERSVRLP FLDSQTGVAQ
60 70 80 90 100
NNCYIWMEKR HRGPGLAPGQ LYTYPARCWR KKRRLHPPED PKLRLLEIKP
110 120 130 140 150
EVELPLKKDG FTSESTTLEA LLRGEGVEKK VDAREEESIQ EIQRVLENDE
160 170 180 190 200
NVEEGNEEED LEEDIPKRKN RTRGRARGSA GGRRRHDAAS QEDHDKPYVC
210 220 230 240 250
DICGKRYKNR PGLSYHYAHT HLASEEGDEA QDQETRSPPN HRNENHRPQK
260 270 280 290 300
GPDGTVIPNN YCDFCLGGSN MNKKSGRPEE LVSCADCGRS GHPTCLQFTL
310 320 330 340 350
NMTEAVKTYK WQCIECKSCI LCGTSENDDQ LLFCDDCDRG YHMYCLNPPV
360 370
AEPPEGSWSC HLCWELLKEK ASAFGCQA
Length:378
Mass (Da):43,084
Last modified:November 25, 2008 - v3
Checksum:i7E6A6FD07A0E4668
GO
Isoform 2 (identifier: Q92784-2) [UniParc]FASTAAdd to basket
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.
Show »
Length:357
Mass (Da):40,244
Checksum:i50914AC52A9AD3FB
GO
Isoform 3 (identifier: Q92784-3) [UniParc]FASTAAdd to basket

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.
Show »
Length:412
Mass (Da):46,401
Checksum:iBB778F504DF34AD9
GO
Isoform 4 (identifier: Q92784-4) [UniParc]FASTAAdd to basket

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

Show »
Length:195
Mass (Da):22,667
Checksum:i48875102247B766B
GO
Isoform 5 (identifier: Q92784-5) [UniParc]FASTAAdd to basket

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

Show »
Length:367
Mass (Da):41,184
Checksum:i6038156FCCD069B2
GO

Sequence cautioni

Isoform 4 : The sequence BAB14838 differs from that shown. Reason: Frameshift at position 187.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti12L → V in AAC50686 (PubMed:8812431).Curated1
Sequence conflicti24C → S in AAC50686 (PubMed:8812431).Curated1
Sequence conflicti32C → S in BAB14838 (PubMed:14702039).Curated1
Sequence conflicti170N → D in BAB14838 (PubMed:14702039).Curated1
Sequence conflicti207Y → H in BAC86753 (PubMed:14702039).Curated1
Sequence conflicti216H → Y in BAC86753 (PubMed:14702039).Curated1
Isoform 5 (identifier: Q92784-5)
Sequence conflicti358S → P in BAH11762 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_047771177R → H.1 PublicationCorresponds to variant rs17855717dbSNPEnsembl.1
Isoform 2 (identifier: Q92784-2)
Natural varianti326H → R in dbSNP: rs17855716. 1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0358821 – 11MATVIHNPLKA → MFYGRINGRNFAASSLPVAF AATPLMLFLPNPQLICSFPI SSRNHITGLMPPGKLKLENL FHMCTR in isoform 3. 1 PublicationAdd BLAST11
Alternative sequenceiVSP_0557481 – 11MATVIHNPLKA → MGFTDLEEPISGCPGGPWAL G in isoform 5. 1 PublicationAdd BLAST11
Alternative sequenceiVSP_035883177 – 378RGSAG…FGCQA → RCPLPSLHCFLPSLCRDRC in isoform 4. 1 PublicationAdd BLAST202
Alternative sequenceiVSP_035884291 – 378GHPTC…FGCQA → AHLGGEGRKEKEAAAAARTT EDLFGSTSESDTSTFHGFDE DDLEEPRSCRGRRSGRGSPT ADKKGSC in isoform 2, isoform 3 and isoform 5. 3 PublicationsAdd BLAST88

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY803021 mRNA. Translation: AAX20019.1.
AK024141 mRNA. Translation: BAB14838.1. Frameshift.
AK126933 mRNA. Translation: BAC86753.1.
AK294425 mRNA. Translation: BAH11762.1.
AC004828 Genomic DNA. No translation available.
AC006360 Genomic DNA. No translation available.
AL392024 Genomic DNA. No translation available.
AC007160 Genomic DNA. No translation available.
BC060801 mRNA. Translation: AAH60801.1.
U43919 Genomic DNA. Translation: AAC50686.1.
CCDSiCCDS45133.1. [Q92784-2]
CCDS61495.1. [Q92784-5]
CCDS61496.1. [Q92784-3]
CCDS61497.1. [Q92784-1]
RefSeqiNP_001267471.1. NM_001280542.1. [Q92784-1]
NP_001267472.1. NM_001280543.1. [Q92784-5]
NP_001267473.1. NM_001280544.1.
NP_036206.3. NM_012074.4. [Q92784-2]
XP_016877159.1. XM_017021670.1. [Q92784-1]
XP_016877160.1. XM_017021671.1. [Q92784-5]
UniGeneiHs.162868.

Genome annotation databases

EnsembliENST00000381216; ENSP00000370614; ENSG00000205683. [Q92784-2]
ENST00000541685; ENSP00000441640; ENSG00000205683. [Q92784-2]
ENST00000546183; ENSP00000444662; ENSG00000205683. [Q92784-5]
ENST00000556509; ENSP00000450518; ENSG00000205683. [Q92784-1]
ENST00000614862; ENSP00000481992; ENSG00000205683. [Q92784-5]
GeneIDi8110.
KEGGihsa:8110.
UCSCiuc001xnc.4. human. [Q92784-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY803021 mRNA. Translation: AAX20019.1.
AK024141 mRNA. Translation: BAB14838.1. Frameshift.
AK126933 mRNA. Translation: BAC86753.1.
AK294425 mRNA. Translation: BAH11762.1.
AC004828 Genomic DNA. No translation available.
AC006360 Genomic DNA. No translation available.
AL392024 Genomic DNA. No translation available.
AC007160 Genomic DNA. No translation available.
BC060801 mRNA. Translation: AAH60801.1.
U43919 Genomic DNA. Translation: AAC50686.1.
CCDSiCCDS45133.1. [Q92784-2]
CCDS61495.1. [Q92784-5]
CCDS61496.1. [Q92784-3]
CCDS61497.1. [Q92784-1]
RefSeqiNP_001267471.1. NM_001280542.1. [Q92784-1]
NP_001267472.1. NM_001280543.1. [Q92784-5]
NP_001267473.1. NM_001280544.1.
NP_036206.3. NM_012074.4. [Q92784-2]
XP_016877159.1. XM_017021670.1. [Q92784-1]
XP_016877160.1. XM_017021671.1. [Q92784-5]
UniGeneiHs.162868.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KWJNMR-A261-372[»]
2KWKNMR-A261-372[»]
2KWNNMR-A261-372[»]
2KWONMR-A261-372[»]
5I3LX-ray1.85A/B254-368[»]
ProteinModelPortaliQ92784.
SMRiQ92784.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113779. 26 interactors.
DIPiDIP-59245N.
STRINGi9606.ENSP00000370614.

PTM databases

iPTMnetiQ92784.
PhosphoSitePlusiQ92784.

Polymorphism and mutation databases

DMDMi215274167.

Proteomic databases

MaxQBiQ92784.
PaxDbiQ92784.
PeptideAtlasiQ92784.
PRIDEiQ92784.

Protocols and materials databases

DNASUi8110.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000381216; ENSP00000370614; ENSG00000205683. [Q92784-2]
ENST00000541685; ENSP00000441640; ENSG00000205683. [Q92784-2]
ENST00000546183; ENSP00000444662; ENSG00000205683. [Q92784-5]
ENST00000556509; ENSP00000450518; ENSG00000205683. [Q92784-1]
ENST00000614862; ENSP00000481992; ENSG00000205683. [Q92784-5]
GeneIDi8110.
KEGGihsa:8110.
UCSCiuc001xnc.4. human. [Q92784-1]

Organism-specific databases

CTDi8110.
DisGeNETi8110.
GeneCardsiDPF3.
HGNCiHGNC:17427. DPF3.
HPAiHPA066790.
MIMi601672. gene.
neXtProtiNX_Q92784.
OpenTargetsiENSG00000205683.
PharmGKBiPA134888535.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1244. Eukaryota.
ENOG410YDAG. LUCA.
GeneTreeiENSGT00530000063194.
HOGENOMiHOG000217918.
HOVERGENiHBG004475.
InParanoidiQ92784.
OMAiVAHAACT.
PhylomeDBiQ92784.
TreeFamiTF318971.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000011332-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ92784.
GenomeRNAii8110.
PROiQ92784.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000205683.
CleanExiHS_DPF3.
ExpressionAtlasiQ92784. baseline and differential.
GenevisibleiQ92784. HS.

Family and domain databases

Gene3Di3.30.160.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR025750. Requiem/DPF_N_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
PF14051. Requiem_N. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
SM00355. ZnF_C2H2. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 2 hits.
PROSITEiPS01359. 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]
ProtoNetiSearch...

Entry informationi

Entry nameiDPF3_HUMAN
AccessioniPrimary (citable) accession number: Q92784
Secondary accession number(s): A8MSI3
, B7Z276, F5H575, Q32UJ0, Q6P9E6, Q6ZT41, Q9H7Y5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 25, 2008
Last modified: November 30, 2016
This is version 130 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.