3U2B | pdb_00003u2b

Structure of the Sox4 HMG domain bound to DNA

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	d3u2bc_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	mouse (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	SCOP2 Family	HMG-box	8073213	4000788	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	HMG-box	8073214	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)
C	HMG_box	e3u2bC1	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)
C	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
C	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
C	Transcription factor SOX-4	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 DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity RNA polymerase II transcription regulatory region sequence-specific DNA 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 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	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of myoblast differentiation cellular process myoblast differentiation positive regulation of cellular process regulation of protein stability regulation of biological quality protein stabilization cardiac chamber morphogenesis heart morphogenesis ventricular septum development anatomical structure morphogenesis cardiac septum development cardiac septum morphogenesis ventricular septum morphogenesis cardiac chamber development animal organ morphogenesis cardiac ventricle development cell development nervous system development glial cell development neurogenesis gliogenesis glial cell differentiation mesenchyme development tissue development 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 sympathetic nervous system development autonomic nervous system development hemopoiesis cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation immune system process T cell differentiation leukocyte differentiation 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 regulation of biosynthetic 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 metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process multicellular organismal-level homeostasis homeostatic process hematopoietic stem cell homeostasis homeostasis of number of cells somatic stem cell population maintenance maintenance of cell number stem cell population maintenance negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular 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 atrioventricular valve development heart valve development mitral valve morphogenesis heart valve morphogenesis mitral valve development atrioventricular valve morphogenesis epithelium development neuroepithelial cell differentiation columnar/cuboidal epithelial cell differentiation epithelial cell differentiation cardiac right ventricle morphogenesis cardiac ventricle morphogenesis positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process chemical homeostasis glucose homeostasis carbohydrate homeostasis generation of neurons noradrenergic neuron differentiation neuron differentiation pro-B cell differentiation lymphoid progenitor cell differentiation hematopoietic progenitor cell differentiation spinal cord development central nervous system development regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation positive regulation of T cell differentiation regulation of cell development positive regulation of cell activation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process positive regulation of T cell activation gamma-delta T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of gamma-delta T cell differentiation positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis regulation of multicellular organismal process regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of gamma-delta T cell activation positive regulation of gamma-delta T cell differentiation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation gamma-delta T cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of gamma-delta T cell activation positive regulation of lymphocyte differentiation regulation of lymphocyte activation aorta morphogenesis blood vessel morphogenesis tube development artery development aorta development vasculature development tube morphogenesis ascending aorta development ascending aorta morphogenesis artery morphogenesis blood vessel development negative regulation of developmental process negative regulation of myoblast differentiation negative regulation of cell differentiation cellular response to stimulus response to stimulus response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis response to monosaccharide response to carbohydrate response to glucose response to chemical cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus signaling regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator regulation of signaling signal transduction by p53 class mediator regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation pancreas development endocrine system development endocrine pancreas development cardiac atrium morphogenesis septum primum development atrial septum primum morphogenesis cardiac atrium development atrial septum morphogenesis atrial septum development positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway positive regulation of signaling regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization localization positive regulation of insulin secretion intracellular protein localization regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion renal system development kidney morphogenesis kidney development glial cell proliferation	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	DNA (5'-D(CPCPAPGPGPAPCPAPAPTPAPGPAPGPAPC)-3')	-	-	-
A	DNA (5'-D(GPTPCPTPCPTPAPTPTPGPTPCPCPTPGPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR017386	Transcription factor SOX-12/11/4	Family
C	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
C	IPR050140	SRY-related HMG-box transcription factor-like	Family
C	IPR009071	High mobility group box domain	Domain

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.