3JUA | pdb_00003jua

Structural basis of YAP recognition by TEAD4 in the Hippo pathway

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
G	d3juag1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	TEAD-like transcription factors, E-set domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d3juag2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3juae1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	TEAD-like transcription factors, E-set domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3juae2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3juac1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	TEAD-like transcription factors, E-set domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3juac2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3juaa1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	TEAD-like transcription factors, E-set domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3juaa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	RVP	e3juaG1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
E	RVP	e3juaE1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
C	RVP	e3juaC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
A	YBD	e3juaA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: HTH	T: winged helix domain	F: YBD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	2.70.50.80	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
E	2.70.50.80	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
C	2.70.50.80	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
A	2.70.50.80	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF15238	Omega loop, TEAD interacting region 3 (TEADIR3)	Omega loop, TEAD interacting region 3	This entry represents the third TEAD interacting region (omega loop) present in YAP/TAZ, FAM181, and PERCC1 families [1-5]. This conserved region is remotely related to the omega loop found in the Vestigial family (VGLL2 and VGLL3) [6].	Domain
A, C, E, G	PF17725	YAP binding domain (YBD)	YAP binding domain	TEA domain transcription factors contain an N-terminal TEA domain Pfam:PF01285 and a C-terminal YAP binding domain (YBD). This entry corresponds to the YBD that binds to the oncoproteins YAP and TAZ. The structure of the YBD shows that it has an Ig-l ...	TEA domain transcription factors contain an N-terminal TEA domain Pfam:PF01285 and a C-terminal YAP binding domain (YBD). This entry corresponds to the YBD that binds to the oncoproteins YAP and TAZ. The structure of the YBD shows that it has an Ig-like beta sandwich fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	65 kDa Yes-associated protein	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 protein binding proline-rich region binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity 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 protein binding proline-rich region binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor 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 chromatin binding transcription coactivator activity transcription corepressor activity transcription factor binding DNA-binding transcription factor binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction Wnt signaling pathway developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular developmental process cell development regulation of neurogenesis regulation of cell differentiation nervous system development regulation of cell development regulation of nervous system development multicellular organism development neurogenesis cell differentiation anatomical structure development regulation of multicellular organismal process system development response to ketone response to lipid response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound negative regulation of stem cell differentiation negative regulation of developmental process negative regulation of biological process stem cell differentiation regulation of stem cell differentiation negative regulation of cellular process negative regulation of cell differentiation regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process regulation of growth positive regulation of cell population proliferation regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation organ growth striated muscle tissue development 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 muscle cell proliferation cardiac muscle tissue growth muscle tissue development positive regulation of developmental growth positive regulation of heart growth striated muscle cell proliferation heart development heart growth cell population proliferation regulation of developmental growth cardiac muscle tissue development positive regulation of organ growth growth animal organ development tissue development circulatory system development positive regulation of growth regulation of cell population proliferation positive regulation of cardiac muscle tissue growth positive regulation of multicellular organismal process regulation of keratinocyte proliferation regulation of epithelial cell proliferation epithelial cell proliferation keratinocyte proliferation cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid cellular response to lipid paraxial mesoderm development mesenchyme development mesoderm development lateral mesoderm development heart morphogenesis embryo development embryonic heart tube development tube morphogenesis embryonic heart tube morphogenesis animal organ morphogenesis epithelial tube morphogenesis embryonic organ development embryonic organ morphogenesis epithelium development tube development embryonic morphogenesis morphogenesis of an epithelium anatomical structure morphogenesis tissue morphogenesis cell morphogenesis tissue regeneration cardiac muscle tissue regeneration regeneration digestive system development intestinal epithelial cell differentiation intestinal epithelial cell development digestive tract development epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development columnar/cuboidal epithelial cell differentiation respiratory tube development lung epithelium development lung epithelial cell differentiation lung cell differentiation lung development respiratory system development somatic stem cell population maintenance maintenance of cell number stem cell population maintenance negative regulation of signaling regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway 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 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 nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process 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 regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process regulation of cellular component organization positive regulation of cell growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis fat cell differentiation negative regulation of fat cell differentiation regulation of fat cell differentiation cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly epidermal cell differentiation epidermis development skin development keratinocyte differentiation regulation of localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization intracellular signal transduction signal transduction in response to DNA damage cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation heart process system process circulatory system process regulation of stem cell population maintenance positive regulation of stem cell population maintenance regulation of epithelial cell differentiation negative regulation of epithelial cell differentiation cell projection organization negative regulation of organelle assembly plasma membrane bounded cell projection assembly negative regulation of plasma membrane bounded cell projection assembly cilium assembly negative regulation of cell projection organization cilium organization organelle assembly plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly organelle organization regulation of cilium assembly negative regulation of organelle organization regulation of organelle assembly negative regulation of cilium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of epithelial cell proliferation kidney epithelium development metanephric nephron tubule epithelial cell differentiation metanephric epithelium development nephron tubule development renal system development metanephros development renal tubule development regulation of epithelial cell differentiation involved in kidney development regulation of nephron tubule epithelial cell differentiation regulation of metanephric nephron tubule epithelial cell differentiation nephron development metanephric nephron epithelium development nephron epithelium development epithelial cell differentiation involved in kidney development metanephric nephron tubule development nephron tubule epithelial cell differentiation cell differentiation involved in kidney development metanephric tubule development kidney development regulation of stem cell proliferation stem cell proliferation interleukin-6-mediated signaling pathway response to interleukin-6 cellular response to interleukin-6 response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to cytokine stimulus blood vessel morphogenesis vasculogenesis vasculature development blood vessel development regulation of osteoblast differentiation osteoblast differentiation positive regulation of osteoblast differentiation ossification positive regulation of cell differentiation notochord development wound healing response to wounding multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway positive regulation of canonical Wnt signaling pathway positive regulation of signaling Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process glucose catabolic process to pyruvate nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process hexose catabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process hexose metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process glucose catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process monosaccharide catabolic process small molecule catabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process monosaccharide metabolic process cellular respiration canonical glycolysis catabolic process ATP metabolic process energy derivation by oxidation of organic compounds glycolytic process through glucose-6-phosphate purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process glycolytic process through fructose-6-phosphate glucose metabolic process negative regulation of gene expression branching morphogenesis of an epithelial tube lung morphogenesis axis elongation bud elongation involved in lung branching branch elongation of an epithelium developmental growth involved in morphogenesis morphogenesis of a branching structure epithelial tube branching involved in lung morphogenesis morphogenesis of a branching epithelium hippo signaling	cellular anatomical structure membrane cell-cell junction anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle mitochondrion organelle cellular anatomical structure membrane cell-cell junction anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen apical junction complex bicellular tight junction tight junction RNA polymerase II transcription regulator complex nuclear protein-containing complex TEAD-YAP complex
A, C, E, G	Transcriptional enhancer factor TEF-3	DNA binding sequence-specific DNA binding 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 DNA binding sequence-specific DNA binding 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 DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development cellular developmental process cell differentiation developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment trophectodermal cell differentiation trophectodermal cell fate commitment regulation of biological process regulation of developmental process biological regulation positive regulation of biological process regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process animal organ development embryonic organ development regulation of cellular process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II hippo signaling cellular response to stimulus response to stimulus signaling intracellular signal transduction cell communication signal transduction	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR051583	Yes-associated protein 1	Family
B, D, F, H	IPR036020	WW domain superfamily	Homologous Superfamily
B, D, F, H	IPR053819	TEAD interacting region 3, omega loop	Conserved Site
B, D, F, H	IPR001202	WW domain	Domain
A, C, E, G	IPR050937	TEC1_TEAD_TF	Unknown
A, C, E, G	IPR038096	TEA/ATTS domain superfamily	Homologous Superfamily
A, C, E, G	IPR000818	TEA/ATTS domain	Domain
A, C, E, G	IPR027255	Transcriptional enhancer factor TEF-3 (TEAD4)	Family
A, C, E, G	IPR016361	Transcriptional enhancer factor, metazoa	Family
A, C, E, G	IPR041086	YAP binding 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.