12YU | pdb_000012yu

Crystal structure of the BPTF PHD finger-Bromodomain bound to H3R2X3K4me3

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00439	Bromodomain (Bromodomain)	Bromodomain	Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].	Domain
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Nucleosome-remodeling factor subunit BPTF	sequence-specific DNA binding DNA binding binding nucleic acid binding	developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development animal gross anatomical part developmental process system development cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development animal gross anatomical part developmental process system development cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome ATPase complex protein-containing complex catalytic complex perinuclear region of cytoplasm cell body nuclear protein-containing complex NURF complex ISWI-type complex SWI/SNF superfamily-type complex
B	H3R2X3K4me3	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038028	Nucleosome-remodeling factor subunit BPTF	Family
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR018359	Bromodomain, conserved site	Conserved Site
A	IPR028941	WHIM2 domain	Domain
A	IPR001487	Bromodomain	Domain
A	IPR018501	DDT domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A	IPR061860	Domain of unknown function DUF8799	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: Q12830	urinary bladder cancer psoriasis tuberculosis attention deficit hyperactivity disorder, inattentive type intellectual disability lung adenocarcinoma medulloblastoma neurodevelopmental disorder with dysmorphic facies and distal limb anomalies oligodendroglioma pancreatic ductal adenocarcinoma rheumatoid arthritis atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant ependymoma metabolic syndrome X urinary bladder cancer psoriasis tuberculosis attention deficit hyperactivity disorder, inattentive type intellectual disability lung adenocarcinoma medulloblastoma neurodevelopmental disorder with dysmorphic facies and distal limb anomalies oligodendroglioma pancreatic ductal adenocarcinoma rheumatoid arthritis atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant ependymoma metabolic syndrome X non-alcoholic fatty liver disease osteosarcoma primitive neuroectodermal tumor spina bifida urinary bladder neoplasm glioblastoma large cell medulloblastoma malignant glioma microcephaly non-small cell lung carcinoma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	A1DEJ	Parent Component: ALA
B	M3L	Parent Component: LYS : AA0074 : N6,N6,N6-trimethyl-L-lysine MOD:00083
B	NH2	: AA0074 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 : N6,N6,N6-trimethyl-L-lysine MOD:00083 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109