1ZAA

ZINC FINGER-DNA RECOGNITION: CRYSTAL STRUCTURE OF A ZIF268-DNA COMPLEX AT 2.1 ANGSTROMS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1zaac1	Small proteins	beta-beta-alpha zinc fingers	beta-beta-alpha zinc fingers	Classic zinc finger, C2H2	ZIF268	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8038885	3001077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8038881	3001077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8038883	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	zf-C2H2_12	e1zaaC1	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	zf-C2H2_17	e1zaaC2	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	zf-C2H2_20	e1zaaC3	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_20	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	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	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	DNA (5'-D(APGPCPGPTPGPGPGPCPGP*T)-3')	-	-	-
C	PROTEIN (ZIF268)	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 chromatin binding promoter-specific chromatin binding hemi-methylated DNA-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 chromatin binding promoter-specific chromatin binding hemi-methylated DNA-binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity 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 protein binding histone acetyltransferase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process protein modification process positive regulation of cellular process regulation of biological process regulation of post-translational protein modification regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process protein modification process positive regulation of cellular process regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process cellular process macromolecule metabolic process post-translational protein modification regulation of metabolic process ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process response to stimulus response to stress response to ischemia cellular response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death regulation of biosynthetic process positive regulation of hormone metabolic process regulation of hormone biosynthetic process regulation of hormone metabolic process regulation of hormone levels hormone metabolic process biosynthetic process positive regulation of biosynthetic process positive regulation of hormone biosynthetic process regulation of biological quality hormone biosynthetic process multicellular organismal process connective tissue development renal system development kidney vasculature development multicellular organism development renal system vasculature development anatomical structure development nephron development system development blood vessel development developmental process cell population proliferation animal organ development cell proliferation involved in kidney development glomerular mesangium development tissue development vasculature development circulatory system development glomerulus development glomerular mesangial cell proliferation glomerulus vasculature development kidney development regulation of steroid biosynthetic process ketone metabolic process steroid metabolic process regulation of lipid metabolic process lipid biosynthetic process C21-steroid hormone metabolic process regulation of small molecule metabolic process progesterone metabolic process small molecule metabolic process steroid biosynthetic process steroid hormone biosynthetic process olefinic compound biosynthetic process small molecule biosynthetic process progesterone biosynthetic process regulation of ketone biosynthetic process regulation of steroid metabolic process C21-steroid hormone biosynthetic process regulation of progesterone biosynthetic process regulation of ketone metabolic process olefinic compound metabolic process regulation of lipid biosynthetic process ketone biosynthetic process lipid metabolic process skeletal muscle cell differentiation cellular developmental process skeletal muscle tissue development striated muscle tissue development muscle structure development skeletal muscle organ development cell differentiation muscle tissue development muscle organ development hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation immune system process T cell differentiation leukocyte differentiation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic 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 nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription circadian regulation of gene expression circadian rhythm positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of gene expression, epigenetic cellular component organization transcription by RNA polymerase II chromatin organization chromatin remodeling cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of chemokine production chemokine production positive regulation of chemokine production response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm cellular response to nitrogen compound response to heparin response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to heparin multicellular organismal-level homeostasis homeostatic process temperature homeostasis circadian temperature homeostasis negative regulation of RNA biosynthetic process 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 positive regulation of transcription by RNA polymerase II metanephric glomerulus vasculature development positive regulation of cell population proliferation metanephric glomerulus development regulation of glomerular mesangial cell proliferation positive regulation of glomerular mesangial cell proliferation metanephros development metanephric glomerular mesangial cell proliferation involved in metanephros development metanephric nephron development regulation of metanephric glomerular mesangial cell proliferation positive regulation of cell proliferation involved in kidney development positive regulation of glomerular metanephric mesangial cell proliferation regulation of cell proliferation involved in kidney development metanephric glomerular mesangium development cell proliferation involved in metanephros development regulation of cell population proliferation response to peptide cellular response to interleukin-8 response to interleukin-8 response to cytokine cellular response to cytokine stimulus cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation cellular response to abiotic stimulus response to gamma radiation neuron apoptotic process regulation of neuron apoptotic process response to hexose response to monosaccharide response to carbohydrate response to glucose response to hormone response to peptide hormone response to insulin cellular response to organic cyclic compound cellular response to mycophenolic acid response to mycophenolic acid response to organic cyclic compound cytokine-mediated signaling pathway cellular response to interleukin-1 interleukin-1-mediated signaling pathway response to interleukin-1 regulation of protein sumoylation peptidyl-lysine modification peptidyl-amino acid modification regulation of protein modification by small protein conjugation or removal protein sumoylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	DNA (5'-D(TPAPCPGPCPCPCPAPCPGP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR013087	Zinc finger C2H2-type	Domain
C	IPR021849	Early growth response, N-terminal	Domain
C	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
C	IPR021839	Early growth response protein 1, C-terminal	Repeat

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.