9U19 | pdb_00009u19

Crystal structure of the NKX2.1 homeodomain in complex with a 12-bp DNA duplex containing a CACG motif variant

External Resource: Annotation

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E	12bp reverse complementary	-	-	-
C, F	Homeobox protein Nkx-2.1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor 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 intronic transcription regulatory region sequence-specific DNA binding enzyme binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development developmental induction regulation of biosynthetic process regulation of biological process regulation of cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development developmental induction 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 cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cerebral cortex cell migration forebrain development pallium development cerebral cortex development telencephalon cell migration forebrain cell migration cell migration telencephalon development cell motility endocrine system development pituitary gland development gland development diencephalon development cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription epithelium development cellular developmental process tube development respiratory tube development lung epithelium development tissue development epithelial cell differentiation lung epithelial cell differentiation lung cell differentiation cell differentiation lung development respiratory system development club cell differentiation negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion anatomical structure morphogenesis anatomical structure formation involved in morphogenesis regulation of epithelial to mesenchymal transition regulation of developmental process regulation of cell differentiation mesenchyme development negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of developmental process negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation negative regulation of multicellular organismal process 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 positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to hormone response to chemical gonad development reproductive system development reproductive process sex differentiation developmental process involved in reproduction male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development Leydig cell differentiation behavior locomotory behavior hippocampus development limbic system development neurogenesis gliogenesis oligodendrocyte differentiation glial cell differentiation phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process lipid metabolic process thyroid gland development endoderm development branching morphogenesis of an epithelial tube tube morphogenesis lung morphogenesis animal organ morphogenesis epithelial tube morphogenesis morphogenesis of an epithelium tissue morphogenesis morphogenesis of a branching structure epithelial tube branching involved in lung morphogenesis morphogenesis of a branching epithelium hypothalamus development cerebral cortex GABAergic interneuron differentiation central nervous system neuron differentiation neuron differentiation GABAergic neuron differentiation forebrain generation of neurons generation of neurons cerebral cortex neuron differentiation forebrain neuron differentiation type II pneumocyte differentiation lung secretory cell differentiation lung saccule development lung alveolus development rhythmic process positive regulation of circadian rhythm circadian rhythm regulation of circadian rhythm axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development forebrain dorsal/ventral pattern formation pattern specification process regionalization dorsal/ventral pattern formation forebrain regionalization globus pallidus development neural nucleus development neuron migration interneuron migration forebrain neuron fate commitment neuron fate commitment cell fate commitment	protein-containing complex transcription regulator complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle protein-containing complex transcription regulator complex intracellular organelle cellular anatomical structure intracellular anatomical structure 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
A, D	CACG-containing 12bp forward strand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C, F	IPR020479	Homeodomain, metazoa	Domain
C, F	IPR001356	Homeodomain	Domain
C, F	IPR050394	Homeobox NK-like transcription regulators	Family
C, F	IPR017970	Homeobox, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: P43699	brain-lung-thyroid syndrome congenital hypothyroidism lung disease non-small cell lung carcinoma thyroid cancer, nonmedullary, 1 hereditary progressive chorea without dementia lung cancer malignant mesothelioma Thyroid Agenesis thyroid gland papillary carcinoma choreatic disease familial nonmedullary thyroid carcinoma hypothyroidism chorea, benign familial congenital diaphragmatic hernia brain-lung-thyroid syndrome congenital hypothyroidism lung disease non-small cell lung carcinoma thyroid cancer, nonmedullary, 1 hereditary progressive chorea without dementia lung cancer malignant mesothelioma Thyroid Agenesis thyroid gland papillary carcinoma choreatic disease familial nonmedullary thyroid carcinoma hypothyroidism chorea, benign familial congenital diaphragmatic hernia intellectual disability cancer

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.