2JP9

Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA

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)
C [auth A]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8043863	3001077	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)
C [auth A]	zf-C2H2_12	e2jp9A1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_12	ECOD (1.6)
C [auth A]	zf-C2H2_17	e2jp9A2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_17	ECOD (1.6)
C [auth A]	zf-C2H2_like	e2jp9A3	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_like	ECOD (1.6)
C [auth A]	zf-C2H2_13	e2jp9A4	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_13	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.30.160.60	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Classic Zinc Finger	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF00096	Zinc finger, C2H2 type (zf-C2H2)	Zinc finger, C2H2 type	The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, an ...	The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	DNA (5'-D(PDCPDGPDCPDGPDGPDGPDGPDGPDCPDGPDTPDCPDTPDGPDCPDGP*DC)-3')	-	-	-
B [auth C]	DNA (5'-D(PDGPDCPDGPDCPDAPDGPDAPDCPDGPDCPDCPDCPDCPDCPDGPDCP*DG)-3')	-	-	-
C [auth A]	Wilms tumor 1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding C2H2 zinc finger domain binding protein domain specific binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding C2H2 zinc finger domain binding protein domain specific binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity hemi-methylated DNA-binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity double-stranded methylated DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development heart development circulatory system development tissue development extracellular matrix organization renal system development glomerular basement membrane development cellular component organization glomerulus development cellular process cellular component organization or biogenesis nephron development kidney development extracellular structure organization external encapsulating structure organization regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process renal filtration cell differentiation kidney epithelium development cellular developmental process glomerular epithelial cell differentiation epithelial cell differentiation cell differentiation nephron epithelium development epithelial cell differentiation involved in kidney development epithelium development glomerular epithelium development cell differentiation involved in kidney development podocyte differentiation positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death regulation of developmental process regulation of gonad development regulation of reproductive process positive regulation of developmental process positive regulation of male gonad development regulation of multicellular organismal process regulation of male gonad development positive regulation of reproductive process positive regulation of gonad development positive regulation of multicellular organismal process regulation of growth regulation of cellular component organization negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth negative regulation of growth negative regulation of cellular process genitalia development male genitalia development cellular response to stimulus response to stimulus cellular response to gonadotropin stimulus response to endogenous stimulus response to gonadotropin cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to hormone stimulus sex determination diaphragm development muscle structure development skeletal muscle organ development respiratory system development muscle organ development metanephric epithelium development metanephros development positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process miRNA transcription regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription adrenal cortex development endocrine system development gland development adrenal cortex formation anatomical structure morphogenesis adrenal gland development anatomical structure formation involved in morphogenesis RNA splicing RNA processing cardiac muscle cell fate commitment muscle cell fate commitment muscle cell differentiation striated muscle tissue development cardiac cell fate commitment muscle tissue development cardiac muscle tissue development cardiac muscle cell differentiation cardiocyte differentiation striated muscle cell differentiation cell fate commitment developmental growth organ growth regulation of organ growth regulation of heart growth positive regulation of developmental growth positive regulation of heart growth heart growth regulation of multicellular organismal development regulation of developmental growth positive regulation of organ growth positive regulation of growth negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II 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 mesonephric epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development animal organ morphogenesis epithelial tube morphogenesis ureteric bud development tube development mesonephros development morphogenesis of an epithelium tissue morphogenesis kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium positive regulation of transcription by RNA polymerase II negative regulation of gonad development development of primary female sexual characteristics regulation of female gonad development negative regulation of female gonad development negative regulation of developmental process female gonad development female sex differentiation negative regulation of reproductive process negative regulation of multicellular organismal process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation negative regulation of gene expression regulation of translation negative regulation of gene expression via chromosomal CpG island methylation chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression, epigenetic regulation of kidney development metanephros morphogenesis positive regulation of metanephric ureteric bud development metanephric part of ureteric bud development regulation of metanephric ureteric bud development regulation of metanephros development posterior mesonephric tubule development sexual reproduction multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism gamete generation germ cell development sensory organ development eye development visual system development camera-type eye development sensory system development visceral serous pericardium development pericardium development negative regulation of programmed cell death negative regulation of apoptotic process regulation of animal organ morphogenesis regulation of animal organ formation animal organ formation regulation of anatomical structure morphogenesis cellular response to nitrogen compound response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to cAMP response to organic cyclic compound blastoderm segmentation zygotic determination of anterior/posterior axis, embryo embryonic pattern specification anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process embryo development regionalization tripartite regional subdivision embryonic axis specification anterior/posterior axis specification thorax and anterior abdomen determination axis specification blood vessel morphogenesis vasculogenesis vasculature development blood vessel development negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation metanephric glomerulus vasculature development connective tissue development metanephric glomerulus development kidney vasculature development negative regulation of cell proliferation involved in kidney development renal system vasculature development regulation of glomerular mesangial cell proliferation metanephric glomerular mesangial cell proliferation involved in metanephros development negative regulation of glomerular mesangial cell proliferation metanephric nephron development regulation of metanephric glomerular mesangial cell proliferation negative regulation of metanephric glomerular mesangial cell proliferation cell proliferation involved in kidney development glomerular mesangium development regulation of cell proliferation involved in kidney development metanephric glomerular mesangium development cell proliferation involved in metanephros development glomerular mesangial cell proliferation glomerulus vasculature development metanephric mesenchyme development mesenchyme development kidney mesenchyme development mesenchymal to epithelial transition metanephric nephron morphogenesis S-shaped body morphogenesis metanephric S-shaped body morphogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol intracellular membraneless organelle nucleolus membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR013087	Zinc finger C2H2-type	Domain
C [auth A]	IPR000976	Wilm's tumour protein, N-terminal	Domain
C [auth A]	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: P19544	Denys-Drash syndrome Frasier syndrome WAGR syndrome kidney Wilms tumor malignant mesothelioma desmoplastic small round cell tumor schwannoma aniridia chronic myelogenous leukemia, BCR-ABL1 positive congenital diaphragmatic hernia nephrotic syndrome, type 4 glioblastoma glomerulonephritis acute myeloid leukemia giant cell glioblastoma Denys-Drash syndrome Frasier syndrome WAGR syndrome kidney Wilms tumor malignant mesothelioma desmoplastic small round cell tumor schwannoma aniridia chronic myelogenous leukemia, BCR-ABL1 positive congenital diaphragmatic hernia nephrotic syndrome, type 4 glioblastoma glomerulonephritis acute myeloid leukemia giant cell glioblastoma leukemia breast carcinoma primary ovarian failure Wilms tumor 1 malignant colon neoplasm malignant peripheral nerve sheath tumor Meacham syndrome osteosarcoma acute promyelocytic leukemia breast cancer cancer Congenital hernia of foramen of Morgagni ovarian cancer endometrial carcinoma peritoneal neoplasm Perlman syndrome 46,XY complete gonadal dysgenesis hereditary Wilms tumor intellectual disability malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm familial nephrotic syndrome 46,XY partial gonadal dysgenesis heart disease aniridia 1 kidney disease lung benign neoplasm colonic neoplasm pancreatic neoplasm prostate cancer hematologic disease uterine corpus leiomyoma benign colon neoplasm lung cancer congenital anemia

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.