2KE1 | pdb_00002ke1

Molecular Basis of non-modified histone H3 tail Recognition by the First PHD Finger of Autoimmune Regulator

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FYVE/PHD zinc finger	8084740	3001459	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PHD_1	e2ke1A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_1	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Autoimmune regulator	translation regulator activity protein binding binding histone binding chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding cation binding translation regulator activity protein binding binding histone binding chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	developmental process thymic T cell selection multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation developmental process thymic T cell selection multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation negative thymic T cell selection anatomical structure development T cell differentiation cellular process negative T cell selection T cell selection leukocyte differentiation humoral immune response response to stimulus immune response central tolerance induction to self antigen immune system development central tolerance induction multicellular organism development tolerance induction to self antigen tolerance induction system development RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity tolerance induction dependent upon immune response T cell tolerance induction adaptive immune response peripheral T cell tolerance induction immune effector process peripheral tolerance induction leukocyte mediated immunity regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of chemokine production regulation of gene expression positive regulation of gene expression chemokine production positive regulation of chemokine production positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription epithelium development animal organ development gland development morphogenesis of an epithelium hematopoietic or lymphoid organ development tissue development tissue morphogenesis anatomical structure morphogenesis thymus epithelium morphogenesis thymus development positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of cell motility regulation of leukocyte migration lymphocyte migration regulation of lymphocyte migration leukocyte migration thymocyte migration regulation of thymocyte migration regulation of locomotion regulation of T cell migration mononuclear cell migration regulation of cell migration cell migration regulation of immune system process T cell migration cell motility regulation of mononuclear cell migration locomotion regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus germ cell nucleus intracellular membrane-bounded organelle female germ cell nucleus male germ cell nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus germ cell nucleus intracellular membrane-bounded organelle female germ cell nucleus male germ cell nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen
B	H3K4me0	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR000770	SAND domain	Domain
A	IPR008087	Autoimmune regulator, AIRE	Family
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR004865	HSR domain	Domain
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR042580	AIRE, PHD finger 2	Domain
A	IPR043563	Nuclear body protein Sp110/Sp140/Sp140L-like	Family
A	IPR010919	SAND-like domain superfamily	Homologous Superfamily
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O43918	candidiasis autoimmune polyendocrine syndrome type 1 skin cancer Autoimmune polyendocrinopathy syndrome, type 1 skin neoplasm rheumatoid arthritis autoimmune polyendocrinopathy X-linked adrenal hypoplasia congenita Addison disease autoimmune disease autoimmune polyendocrinopathy type 2 hypoparathyroidism nail disease psoriasis alopecia areata candidiasis autoimmune polyendocrine syndrome type 1 skin cancer Autoimmune polyendocrinopathy syndrome, type 1 skin neoplasm rheumatoid arthritis autoimmune polyendocrinopathy X-linked adrenal hypoplasia congenita Addison disease autoimmune disease autoimmune polyendocrinopathy type 2 hypoparathyroidism nail disease psoriasis alopecia areata autoimmune polyendocrinopathy type 3 celiac disease inflammatory bowel disease oral candidiasis ulcerative colitis ankylosing spondylitis Crohn disease intellectual disability

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.