2LE4

Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2le4a1	All alpha proteins	HMG-box	HMG-box	HMG-box	Sox-2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2le4a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HMG-box	8037201	3001368	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	HMG_box	e2le4A1	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	PF12336	SOX transcription factor (SOXp)	SOX transcription factor	-	Family
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-2	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 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 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 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 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 regulatory RNA binding RNA binding miRNA binding	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation head development forebrain development endocrine system development pituitary gland development animal organ development gland development brain development diencephalon development central nervous system development adenohypophysis development gliogenesis glial cell differentiation glial cell fate commitment cell fate commitment ear development sensory organ development inner ear development regulation of biosynthetic process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway 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 tissue regeneration developmental growth growth regeneration positive regulation of biological process positive regulation of developmental process positive regulation of cell differentiation positive regulation of cellular process response to decreased oxygen levels response to nutrient levels response to oxygen levels response to abiotic stimulus response to oxygen-glucose deprivation 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 organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription response to stress response to wounding somatic stem cell population maintenance maintenance of cell number stem cell population maintenance negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound 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 cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process neuronal stem cell population maintenance protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis ossification osteoblast differentiation regulation of myofibroblast cell apoptotic process regulation of apoptotic process myofibroblast cell apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion anatomical structure morphogenesis positive regulation of cell communication positive regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade positive regulation of signaling response to endogenous stimulus response to growth factor eye development visual system development sensory system development formation of primary germ layer endodermal cell fate specification embryonic morphogenesis cell fate specification embryo development tissue development gastrulation cell fate commitment involved in formation of primary germ layer endoderm development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell fate commitment endodermal cell differentiation regulation of cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition negative regulation of cell cycle process cell cycle G1/S phase transition negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process regulation of catalytic activity regulation of protein metabolic process regulation of peptidase activity regulation of molecular function regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of proteolysis proteolysis regulation of hydrolase activity regulation of endopeptidase activity protein metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol protein-containing complex transcription regulator complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
A	IPR022097	Transcription factor SOX	Family
A	IPR009071	High mobility group box domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P48431	microphthalmia squamous cell carcinoma esophageal squamous cell carcinoma septooptic dysplasia Anophthalmos panhypopituitarism spindle cell sarcoma non-small cell lung carcinoma prostate cancer sarcoma anophthalmia/microphthalmia-esophageal atresia syndrome small cell lung carcinoma primitive neuroectodermal tumor glioblastoma intellectual disability microphthalmia squamous cell carcinoma esophageal squamous cell carcinoma septooptic dysplasia Anophthalmos panhypopituitarism spindle cell sarcoma non-small cell lung carcinoma prostate cancer sarcoma anophthalmia/microphthalmia-esophageal atresia syndrome small cell lung carcinoma primitive neuroectodermal tumor glioblastoma intellectual disability small cell carcinoma large cell medulloblastoma lung cancer astrocytic tumor brain disease breast disease neoplasm of thorax coloboma epithelioid sarcoma osteogenesis imperfecta pituitary cancer esophageal atresia/tracheoesophageal fistula hypopituitarism isolated microphthalmia 1 lung adenocarcinoma lung carcinoma thoracic cancer attention deficit hyperactivity disorder, inattentive type malignant ependymoma bone disease cancer oligodendroglioma esophageal adenocarcinoma pancreatic intraductal papillary-mucinous carcinoma Kallmann syndrome lung benign neoplasm subependymal giant cell astrocytoma lung disease atypical teratoid rhabdoid tumor malignant glioma brain cancer medulloblastoma neoplasm of esophagus cataract cystic fibrosis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.