4EUW | pdb_00004euw

Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution

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	SCOP2 Family	HMG-box	8073207	4000788	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HMG-box	8073208	3001368	SCOP2 (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	HMG_box	e4euwA1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: HMG_box	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transcription factor SOX-9	sequence-specific DNA binding DNA binding binding nucleic acid binding sequence-specific double-stranded DNA binding double-stranded 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 beta-catenin binding protein binding transcription cis-regulatory region binding sequence-specific DNA binding DNA binding binding nucleic acid binding sequence-specific double-stranded DNA binding double-stranded 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 beta-catenin binding protein binding transcription cis-regulatory region binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding pre-mRNA binding RNA binding pre-mRNA intronic binding transcription factor binding bHLH transcription factor binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding protein kinase A catalytic subunit binding protein kinase A binding kinase binding enzyme binding protein kinase binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development heart development circulatory system development cellular developmental process endochondral bone morphogenesis developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development heart development circulatory system development cellular developmental process endochondral bone morphogenesis anatomical structure morphogenesis chondrocyte differentiation involved in endochondral bone morphogenesis cell differentiation chondrocyte differentiation skeletal system morphogenesis animal organ morphogenesis cellular process cartilage development involved in endochondral bone morphogenesis bone morphogenesis bone development developmental cell growth developmental growth chondrocyte hypertrophy growth cell development cell growth chondrocyte development ossification bone mineralization biomineral tissue development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication signal transduction Wnt signaling pathway tube development lung smooth muscle development respiratory tube development smooth muscle tissue development lung development respiratory system development muscle tissue development response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid response to chemical cellular response to lipid mammary gland development gland development heart valve development heart valve morphogenesis stem cell fate commitment chordate embryonic development mesenchyme development embryo development neural crest formation embryo development ending in birth or egg hatching neural crest cell fate commitment neural crest cell differentiation stem cell fate specification neural crest cell fate specification cell fate specification epithelial to mesenchymal transition stem cell differentiation anatomical structure formation involved in morphogenesis mesenchymal cell differentiation cell fate commitment kidney epithelium development regulation of developmental process nephron morphogenesis renal vesicle morphogenesis nephron epithelium morphogenesis positive regulation of biological process renal vesicle development regulation of kidney development developmental induction renal system development positive regulation of developmental process positive regulation of morphogenesis of an epithelium regulation of morphogenesis of an epithelium regulation of multicellular organismal process nephron development regulation of anatomical structure morphogenesis nephron epithelium development epithelium development regulation of animal organ morphogenesis morphogenesis of an epithelium positive regulation of kidney development renal vesicle induction tissue morphogenesis kidney morphogenesis positive regulation of animal organ morphogenesis positive regulation of multicellular organismal process kidney development renal vesicle formation cell population proliferation homeostatic process homeostasis of number of cells within a tissue tissue homeostasis multicellular organismal-level homeostasis regulation of cell proliferation involved in tissue homeostasis regulation of cell population proliferation anatomical structure homeostasis homeostasis of number of cells negative regulation of mesenchymal cell apoptotic process mesenchymal cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of mesenchymal cell apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular response to nitrogen compound response to heparin response to nitrogen compound cellular response to heparin somatic stem cell population maintenance maintenance of cell number stem cell population maintenance system process epithelial structure maintenance digestive system process intestinal epithelial structure maintenance maintenance of gastrointestinal epithelium digestion RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic 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 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process Notch signaling pathway response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1 bronchus development bronchus cartilage development photoreceptor cell differentiation regulation of cell differentiation neurogenesis neuron differentiation negative regulation of cell differentiation negative regulation of developmental process nervous system development regulation of photoreceptor cell differentiation generation of neurons negative regulation of photoreceptor cell differentiation negative regulation of multicellular organismal process negative regulation of neuron differentiation regulation of neuron differentiation prostate gland development reproductive process organ growth developmental process involved in reproduction prostate gland epithelium morphogenesis gland morphogenesis epithelial cell proliferation involved in prostatic bud elongation reproductive structure development prostate gland morphogenetic growth epithelial cell proliferation prostate gland growth axis elongation reproductive system development branch elongation of an epithelium epithelial cell proliferation involved in prostate gland development urogenital system development developmental growth involved in morphogenesis prostate gland morphogenesis primary prostatic bud elongation morphogenesis of a branching structure morphogenesis of a branching epithelium sex differentiation epithelial cell differentiation Sertoli cell differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics gonad development cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis lung epithelium development type I pneumocyte differentiation lung epithelial cell differentiation lung cell differentiation ureter development ureter urothelium development mesonephric epithelium development branching morphogenesis of an epithelial tube nephron tubule morphogenesis regulation of branching involved in ureteric bud morphogenesis tube morphogenesis regulation of morphogenesis of a branching structure mesonephric tubule development renal tubule morphogenesis nephron tubule development ureteric bud morphogenesis branching involved in ureteric bud morphogenesis renal tubule development epithelial tube morphogenesis ureteric bud development mesonephros development positive regulation of branching involved in ureteric bud morphogenesis mesonephric tubule morphogenesis intracellular signal transduction intracellular signaling cassette MAPK cascade ERK1 and ERK2 cascade regulation of cellular component organization positive regulation of cellular component organization positive regulation of cellular component biogenesis positive regulation of extracellular matrix organization extracellular matrix organization regulation of cellular component biogenesis regulation of extracellular matrix assembly positive regulation of extracellular matrix assembly regulation of extracellular matrix organization extracellular matrix assembly positive regulation of cellular process extracellular structure organization external encapsulating structure organization digestive system development intestinal epithelial cell differentiation digestive tract development columnar/cuboidal epithelial cell differentiation lung morphogenesis epithelial tube branching involved in lung morphogenesis epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process positive regulation of mesenchymal cell proliferation positive regulation of cell population proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation catabolic process positive regulation of protein metabolic process macromolecule catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process heart morphogenesis cell proliferation involved in heart morphogenesis regulation of branching involved in lung morphogenesis protein-DNA complex assembly protein-DNA complex organization chromatin organization chromatin remodeling nucleosome assembly nucleosome organization aortic valve development semi-lunar valve development aortic valve morphogenesis negative regulation of miRNA transcription miRNA transcription regulation of miRNA metabolic process miRNA metabolic process negative regulation of miRNA metabolic process regulation of miRNA transcription positive regulation of cell proliferation involved in heart morphogenesis regulation of cell proliferation involved in heart morphogenesis response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus ear morphogenesis embryonic organ morphogenesis ear development sensory organ development embryonic morphogenesis sensory organ morphogenesis inner ear development cochlea development inner ear morphogenesis cochlea morphogenesis embryonic organ development heart valve formation notochord development response to fatty acid cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to epidermal growth factor stimulus response to epidermal growth factor response to growth factor primary sex determination male germ-line sex determination germ-line sex determination primary sex determination, germ-line sex determination male sex determination regulation of cartilage development regulation of chondrocyte differentiation negative regulation of cartilage development negative regulation of chondrocyte differentiation regulation of multicellular organismal development negative regulation of gene expression exocrine system development lacrimal gland development regulation of ossification negative regulation of ossification anterior head development head development cellular response to BMP stimulus response to BMP positive regulation of locomotion regulation of cell motility positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion trachea cartilage development trachea development cell adhesion regulation of cell adhesion spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation otic vesicle development tube formation epithelial tube formation otic vesicle formation otic vesicle morphogenesis limb development appendage development limb bud formation appendage morphogenesis limb morphogenesis regulation of epithelial cell differentiation positive regulation of cell differentiation positive regulation of epithelial cell differentiation epithelial cell proliferation involved in lung morphogenesis regulation of epithelial cell proliferation involved in lung morphogenesis regulation of epithelial cell proliferation Harderian gland development positive regulation of macromolecule biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process eye development retina development in camera-type eye visual system development camera-type eye development sensory system development negative regulation of cellular component organization regulation of beta-catenin-TCF complex assembly negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly negative regulation of beta-catenin-TCF complex assembly beta-catenin-TCF complex assembly negative regulation of signaling regulation of canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway regulation of signaling 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 negative regulation of fatty acid oxidation negative regulation of small molecule metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process organic acid metabolic process regulation of fatty acid oxidation fatty acid oxidation regulation of small molecule metabolic process small molecule metabolic process lipid oxidation fatty acid metabolic process negative regulation of fatty acid metabolic process carboxylic acid metabolic process lipid modification regulation of ketone metabolic process regulation of fatty acid metabolic process monocarboxylic acid metabolic process negative regulation of lipid metabolic process lipid metabolic process regulation of gonad development regulation of reproductive process positive regulation of male gonad development regulation of male gonad development positive regulation of reproductive process positive regulation of gonad development regulation of stem cell proliferation positive regulation of stem cell proliferation stem cell proliferation astrocyte differentiation astrocyte fate commitment central nervous system development gliogenesis glial cell differentiation glial cell fate commitment cell aggregation cartilage condensation embryonic epithelial tube formation metanephric tubule morphogenesis metanephros development metanephros morphogenesis metanephric nephron tubule development metanephric tubule development metanephric tubule formation metanephric epithelium development nephron tubule formation metanephric nephron tubule morphogenesis metanephric nephron development metanephric nephron epithelium development morphogenesis of embryonic epithelium metanephric nephron tubule formation metanephric nephron morphogenesis positive regulation of chondrocyte proliferation chondrocyte proliferation organelle organization cytoskeleton organization cell surface receptor protein tyrosine kinase signaling pathway ERBB signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway negative regulation of immune system process immune system process regulation of immune system process Sertoli cell development epithelial cell development negative regulation of cell population proliferation negative regulation of epithelial cell proliferation 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 positive regulation of cartilage development ureter morphogenesis neuron fate commitment neuron fate specification oligodendrocyte differentiation response to transforming growth factor beta cellular response to transforming growth factor beta stimulus liver development common bile duct development hepaticobiliary system development intrahepatic bile duct development muscle structure development negative regulation of myoblast differentiation regulation of myoblast differentiation myoblast differentiation regulation of osteoblast differentiation negative regulation of osteoblast differentiation osteoblast differentiation positive regulation of mesenchymal stem cell differentiation positive regulation of stem cell differentiation regulation of stem cell differentiation mesenchymal stem cell differentiation regulation of mesenchymal stem cell differentiation regulation of cell cycle process cell cycle regulation of cell cycle cell cycle process glial cell fate specification negative regulation of epithelial cell differentiation positive regulation of chondrocyte differentiation positive regulation of epithelial cell proliferation pancreas development endocrine system development endocrine pancreas development growth plate cartilage chondrocyte development growth plate cartilage development endochondral bone growth growth plate cartilage chondrocyte growth chondrocyte development involved in endochondral bone morphogenesis growth plate cartilage chondrocyte differentiation bone growth mesenchyme morphogenesis endocardial cushion morphogenesis endocardial cushion development neural retina development eye morphogenesis eye photoreceptor cell differentiation camera-type eye morphogenesis camera-type eye photoreceptor cell differentiation retina morphogenesis in camera-type eye retinal rod cell differentiation negative regulation of biomineral tissue development regulation of biomineral tissue development glandular epithelial cell differentiation smooth muscle cell differentiation ureter smooth muscle development muscle cell differentiation ureter smooth muscle cell differentiation cell-cell adhesion stem cell development neural crest cell development localization protein localization to organelle macromolecule localization protein localization to nucleus intracellular protein localization regulation of bone mineralization negative regulation of bone mineralization	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
C	DNA (5'-D(CPTPTPCPTPCPAPAPAPGPAPG)-3')	-	-	-
B	DNA (5'-D(CPTPCPTPTPTPGPAPGPAPAPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
A	IPR022151	Sox developmental protein N-terminal	Domain
A	IPR050917	SOX Transcription Factors	Family
A	IPR009071	High mobility group box domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P48436	campomelic dysplasia 46,XY complete gonadal dysgenesis 46,XY sex reversal 10 carcinoma 46,XX ovotesticular disorder of sex development 46,XX testicular disorder of sex development sarcomatoid carcinoma nonsyndromic congenital nail disorder 4 Craniofacial Abnormalities osteochondrodysplasia otospondylomegaepiphyseal dysplasia, autosomal dominant 46,XX sex reversal 2 46,XY partial gonadal dysgenesis nephrosclerosis osteoarthritis campomelic dysplasia 46,XY complete gonadal dysgenesis 46,XY sex reversal 10 carcinoma 46,XX ovotesticular disorder of sex development 46,XX testicular disorder of sex development sarcomatoid carcinoma nonsyndromic congenital nail disorder 4 Craniofacial Abnormalities osteochondrodysplasia otospondylomegaepiphyseal dysplasia, autosomal dominant 46,XX sex reversal 2 46,XY partial gonadal dysgenesis nephrosclerosis osteoarthritis osteosarcoma esophageal adenocarcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pituitary cancer large cell medulloblastoma lung cancer Alzheimer disease malignant colon neoplasm malignant mesothelioma medulloblastoma Down syndrome glioblastoma pancreatic intraductal papillary-mucinous carcinoma Pick disease 46,XX sex reversal 1 intellectual disability primitive neuroectodermal tumor lung adenocarcinoma malignant ependymoma astrocytic tumor breast cancer mammary neoplasms, animal cancer mucopolysaccharidosis type 4 cervical cancer oligodendroglioma cystic fibrosis osteogenesis imperfecta ductal breast carcinoma in situ ovarian cancer pancreatic intraductal papillary-mucinous neoplasm gonadal dysgenesis isolated Pierre-Robin syndrome psoriasis lung benign neoplasm undifferentiated carcinoma adrenoleukodystrophy major depressive disorder malignant glioma autism spectrum disorder malignant pancreatic neoplasm

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.