2X6V | pdb_00002x6v

Crystal structure of human TBX5 in the DNA-bound and DNA-free form

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)
B	d2x6vb_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	T-box	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2x6va_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	T-box	automated matches	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)
B	SCOP2B Superfamily	p53-like transcription factors	8062621	3000758	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	p53-like transcription factors	8062621	3000758	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)
B	T-box	e2x6vB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: T-box	ECOD (1.6)
A	T-box	e2x6vA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: T-box	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.820	Mainly Beta	Sandwich	Immunoglobulin-like	Transcription factor, T-box	CATH (4.3.0)
A	2.60.40.820	Mainly Beta	Sandwich	Immunoglobulin-like	Transcription factor, T-box	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00907	T-box (T-box)	T-box	The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. ...	The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	5'-D(TPAPAPGPGPTPGPTPGPAP*GP)-3'	-	-	-
C	5'-D(TPCPTPCPAPCPAPCPCPTP*TP)-3'	-	-	-
A, B	T-BOX TRANSCRIPTION FACTOR TBX5	sequence-specific DNA binding DNA binding binding 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 transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding double-stranded DNA binding sequence-specific DNA binding DNA binding binding 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 transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding	multicellular organismal process cellular developmental process vasculogenesis multicellular organism development tube morphogenesis cell differentiation anatomical structure development cell migration cell motility blood vessel development system development cell migration involved in vasculogenesis developmental process heart development multicellular organismal process cellular developmental process vasculogenesis multicellular organism development tube morphogenesis cell differentiation anatomical structure development cell migration cell motility blood vessel development system development cell migration involved in vasculogenesis developmental process heart development blood vessel morphogenesis tube development animal organ development cell migration involved in coronary vasculogenesis cell migration involved in heart development coronary vasculature development vasculature development circulatory system development anatomical structure morphogenesis vasculogenesis involved in coronary vascular morphogenesis cellular process coronary vasculature morphogenesis cell fate specification cell fate commitment heart process bundle of His cell to Purkinje myocyte communication system process regulation of biological process bundle of His cell to Purkinje myocyte communication by electrical coupling regulation of heart contraction regulation of system process biological regulation cell communication by electrical coupling involved in cardiac conduction cell communication by electrical coupling cell communication circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process cell communication involved in cardiac conduction heart contraction blood circulation pattern specification process limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development forelimb morphogenesis appendage morphogenesis limb morphogenesis cardiac left ventricle formation cardiac chamber morphogenesis heart morphogenesis cardiac ventricle formation cardiac chamber formation cardiac ventricle morphogenesis cardiac chamber development anatomical structure formation involved in morphogenesis animal organ morphogenesis cardiac left ventricle morphogenesis cardiac ventricle development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth tissue development striated muscle tissue development muscle cell proliferation cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation regulation of cellular process positive regulation of cellular component organization regulation of cellular component organization gap junction assembly positive regulation of biological process cellular component biogenesis cellular component organization cellular component assembly positive regulation of gap junction assembly cell junction assembly cellular component organization or biogenesis positive regulation of cellular process cell-cell junction assembly cell-cell junction organization positive regulation of cellular component biogenesis regulation of gap junction assembly regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization tissue morphogenesis epithelium development morphogenesis of an epithelium regulation of membrane depolarization membrane depolarization regulation of biological quality regulation of atrial cardiac muscle cell membrane depolarization regulation of membrane potential regulation of growth positive regulation of cell population proliferation regulation of developmental process regulation of cardiac muscle tissue growth positive regulation of developmental process positive regulation of cardiac muscle cell proliferation regulation of organ growth regulation of heart growth regulation of cardiac muscle cell proliferation positive regulation of developmental growth positive regulation of heart growth regulation of multicellular organismal development regulation of developmental growth positive regulation of organ growth positive regulation of growth regulation of cell population proliferation positive regulation of cardiac muscle tissue growth positive regulation of multicellular organismal process positive regulation of cell communication regulation of cell communication by electrical coupling involved in cardiac conduction positive regulation of cell communication by electrical coupling regulation of cell communication by electrical coupling positive regulation of cell communication by electrical coupling involved in cardiac conduction regulation of cell communication signaling cell-cell signaling negative regulation of biological process negative regulation of cardiac muscle tissue growth negative regulation of organ growth negative regulation of growth negative regulation of cellular process negative regulation of cell population proliferation negative regulation of heart growth negative regulation of developmental process negative regulation of developmental growth negative regulation of multicellular organismal process negative regulation of cardiac muscle cell proliferation regulation of cardiac conduction positive regulation of cardiac conduction 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 regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development negative regulation of cell differentiation negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation cardiac muscle cell development cell development muscle cell differentiation cardiac pacemaker cell development muscle structure development striated muscle cell development muscle cell development atrioventricular node development atrioventricular node cell development cardiac cell development cardiac conduction system development atrioventricular node cell differentiation cardiac muscle cell differentiation cardiocyte differentiation cardiac septum development striated muscle cell differentiation cardiac pacemaker cell differentiation cardiac septum cell differentiation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process endocardial cushion development regulation of cardioblast differentiation positive regulation of cell differentiation positive regulation of cardiocyte differentiation regulation of stem cell differentiation positive regulation of cardioblast differentiation positive regulation of stem cell differentiation cardioblast differentiation stem cell differentiation regulation of cardiocyte differentiation bundle of His development ventricular cardiac muscle tissue development His-Purkinje system development pericardium development cardiac muscle cell fate commitment muscle cell fate commitment cardiac cell fate commitment cardiac pacemaker cell fate commitment atrioventricular node cell fate commitment ventricular septum development cardiac atrium morphogenesis cardiac atrium development cardiac septum morphogenesis atrial septum morphogenesis atrial septum development atrioventricular bundle cell differentiation His-Purkinje system cell differentiation respiratory tube development lung development respiratory system development atrial cardiac muscle tissue development sinoatrial node development atrioventricular valve development heart valve development heart valve morphogenesis atrioventricular valve morphogenesis cardioblast proliferation regulation of cardioblast proliferation animal organ formation regulation of secondary heart field cardioblast proliferation heart formation positive regulation of secondary heart field cardioblast proliferation cell proliferation involved in heart morphogenesis regulation of cell proliferation involved in heart morphogenesis	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex transcription regulator complex 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 protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001699	T-box transcription factor	Family
A, B	IPR036960	T-box superfamily	Homologous Superfamily
A, B	IPR046360	T-box transcription factor, DNA-binding domain	Domain
A, B	IPR018186	Transcription factor, T-box, conserved site	Conserved Site
A, B	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q99593	Holt-Oram syndrome atrial fibrillation familial atrial fibrillation cardiomyopathy aortic valve disease 2 lung adenocarcinoma non-small cell lung carcinoma Wildervanck syndrome heart disease intellectual disability lung cancer polydactyly heart, malformation of large cell medulloblastoma lung carcinoma Holt-Oram syndrome atrial fibrillation familial atrial fibrillation cardiomyopathy aortic valve disease 2 lung adenocarcinoma non-small cell lung carcinoma Wildervanck syndrome heart disease intellectual disability lung cancer polydactyly heart, malformation of large cell medulloblastoma lung carcinoma Radial club hand

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.