5SZC

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PHD	e5szcA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)
A	PHD_5	e5szcA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain
B [auth H]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Zinc finger protein DPF3	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process positive regulation of metabolic process positive regulation of DNA repair heterocycle metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process positive regulation of metabolic process positive regulation of DNA repair heterocycle metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process DNA metabolic process organic cyclic compound metabolic process positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of response to stimulus organic substance metabolic process cellular response to stress response to stress regulation of response to stress nitrogen compound metabolic process positive regulation of cellular process DNA repair biological regulation regulation of macromolecule metabolic process positive regulation of double-strand break repair nucleic acid metabolic process regulation of DNA repair positive regulation of nitrogen compound metabolic process DNA damage response cellular process cellular aromatic compound metabolic process regulation of chromosome segregation regulation of cell cycle phase transition regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of cell cycle process chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition developmental process regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation myoblast differentiation nucleotide-excision repair regulation of nucleotide-excision repair multicellular organism development multicellular organismal process nervous system development system development regulation of G0 to G1 transition G0 to G1 transition cellular biosynthetic process RNA metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription animal organ development muscle organ development regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex nucleus nuclear protein-containing complex chromatin chromosome intracellular membrane-bounded organelle cellular anatomical entity nBAF complex intracellular organelle membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex nucleus nuclear protein-containing complex chromatin chromosome intracellular membrane-bounded organelle cellular anatomical entity nBAF complex intracellular organelle organelle intracellular non-membrane-bounded organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle brahma complex SWI/SNF complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth H]	Histone H3 tail peptide	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR013087	Zinc finger C2H2-type	Domain
A	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR025750	DPF1-3, N-terminal domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth H]	IPR009072	Histone-fold	Homologous Superfamily
B [auth H]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth H]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q92784	atrial fibrillation malignant glioma peripheral nervous system disease renal cell carcinoma cystic fibrosis medulloblastoma peripheral neuropathy ulcerative colitis intellectual disability osteosarcoma pituitary cancer
B [auth H]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H]	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064
B [auth H]	MLZ	Parent Component: LYS RESID: AA0055 , AA0076 PSI-MOD : N6-acetyl-L-lysine MOD:00064 , N6-methyl-L-lysine MOD:00085

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.