8CDN | pdb_00008cdn

Crystal structure of human Brachyury in complex with a single T box binding element DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	SCOP2B Superfamily	p53-like transcription factors	8062625	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)
A	F_UNCLASSIFIED	e8cdnA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	T-box transcription factor T	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific	developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment regulation of cellular process negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment regulation of cellular process negative regulation of DNA-binding transcription factor activity 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 regulation of biological process negative regulation of molecular function biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process anatomical structure development tissue development mesoderm development somitogenesis multicellular organismal process epithelium development chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo development regionalization multicellular organism development anatomical structure morphogenesis embryo development ending in birth or egg hatching somite development anatomical structure formation involved in morphogenesis blastoderm segmentation embryonic pattern specification anterior/posterior axis specification, embryo tripartite regional subdivision embryonic axis specification anterior/posterior axis specification axis specification cellular response to stimulus response to stimulus signaling signal transduction cell communication heart development heart morphogenesis animal organ development circulatory system development animal organ morphogenesis system development cardiac muscle cell myoblast differentiation cardiocyte differentiation muscle structure development cardioblast differentiation stem cell differentiation myoblast differentiation transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process 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 biological process 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 cellular 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 RNA biosynthetic process formation of primary germ layer mesoderm morphogenesis embryonic morphogenesis gastrulation tissue morphogenesis mesoderm formation primitive streak formation gastrulation with mouth forming second	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome
B [auth C]	DNA (5'-D(APGPGPTPGPTPGPAPGPCPCPT)-3')	-	-	-
C [auth D]	DNA (5'-D(APGPGPCPTPCPAPCPAPCPCPT)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001699	T-box transcription factor	Family
A	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A	IPR036960	T-box superfamily	Homologous Superfamily
A	IPR046360	T-box transcription factor, DNA-binding domain	Domain
A	IPR002070	Transcription factor, Brachyury	Family
A	IPR018186	Transcription factor, T-box, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O15178	chordoma sacral agenesis-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome neural tube defects, susceptibility to neural tube defect Acrania craniorachischisis iniencephaly psoriasis tethered spinal cord syndrome atypical teratoid rhabdoid tumor diastematomyelia neurenteric cyst pulmonary hypertension osteosarcoma

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.