8CTG | pdb_00008ctg

Extracellular architecture of an engineered canonical Wnt signaling ternary complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Proto-oncogene Wnt3, C-terminal domain-like	8093180	3002689	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Serum amyloid A (SAA)-like	8093177	3002198	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Frizzled domain-like	8034042	3001950	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)
C	F_UNCLASSIFIED	e8ctgC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8ctgC4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8ctgB1	A: alpha arrays	X: Protein Wnt-8 (From Topology)	H: Protein Wnt-8 (From Topology)	T: Protein Wnt-8	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8ctgA1	A: few secondary structure elements	X: Frizzled cysteine-rich domain-related (From Topology)	H: Frizzled cysteine-rich domain-related (From Topology)	T: Frizzled cysteine-rich domain-related	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain
C	PF00058	Low-density lipoprotein receptor repeat class B (Ldl_recept_b)	Low-density lipoprotein receptor repeat class B	-	Repeat
B	PF00110	wnt family (wnt)	wnt family	-	Family
A	PF01392	Fz domain (Fz)	Fz domain	Also known as the CRD (cysteine rich domain), the C6 box in MuSK receptor. This domain of unknown function has been independently identified by several groups [1,2,3,4]. The domain contains 10 conserved cysteines.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Low-density lipoprotein receptor-related protein 6	protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity coreceptor activity toxin transmembrane transporter activity transporter activity transmembrane transporter activity enzyme regulator activity molecular function inhibitor activity molecular function regulator activity protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity coreceptor activity toxin transmembrane transporter activity transporter activity transmembrane transporter activity enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity kinase inhibitor activity kinase regulator activity G protein-coupled receptor binding frizzled binding lipoprotein particle receptor activity low-density lipoprotein particle receptor activity cargo receptor activity identical protein binding protein homodimerization activity protein dimerization activity protein kinase inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity Wnt-protein binding	regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus response to sterol response to stimulus response to lipid response to alcohol regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus response to sterol response to stimulus response to lipid response to alcohol response to oxygen-containing compound response to cholesterol cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to lipid cellular response to sterol cellular response to cholesterol positive regulation of cytosolic calcium ion concentration regulation of biological quality developmental process neural crest cell differentiation cellular developmental process animal organ development mesenchyme development tissue development stem cell differentiation cell differentiation anatomical structure development mesenchymal cell differentiation response to hormone response to endogenous stimulus response to peptide hormone response to nitrogen compound cell surface receptor signaling pathway signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway localization import into cell transport endocytosis establishment of localization vesicle-mediated transport protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane multicellular organismal process chordate embryonic development embryo development neural crest formation epithelial to mesenchymal transition multicellular organism development anatomical structure morphogenesis embryo development ending in birth or egg hatching anatomical structure formation involved in morphogenesis nervous system development system development trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission 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 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 primary metabolic process regulation of macromolecule metabolic process 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 head development dopaminergic neuron differentiation brain development generation of neurons neurogenesis central nervous system neuron differentiation central nervous system development neuron differentiation midbrain development midbrain dopaminergic neuron differentiation cell adhesion cell-cell adhesion transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II muscle cell apoptotic process smooth muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of muscle cell apoptotic process regulation of programmed cell death cell death regulation of smooth muscle cell apoptotic process negative regulation of smooth muscle cell apoptotic process negative regulation of apoptotic process negative regulation of muscle cell apoptotic process negative regulation of cellular process apoptotic process programmed cell death	cell surface cellular anatomical structure cell periphery plasma membrane membrane membrane microdomain membrane raft protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane protein complex Wnt signalosome membrane-bounded organelle intracellular organelle cell surface cellular anatomical structure cell periphery plasma membrane membrane membrane microdomain membrane raft protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane protein complex Wnt signalosome membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle extracellular region endosome membrane early endosome endosome early endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane synapse cell junction somatodendritic compartment cell body neuronal cell body endoplasmic reticulum
B	Protein Wnt-8	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity enzyme binding protease binding G protein-coupled receptor binding frizzled binding	developmental process multicellular organism development multicellular organismal process anterior/posterior axis specification anatomical structure development anterior/posterior pattern specification pattern specification process axis specification regionalization tissue development mesoderm development cellular response to stimulus regulation of biological process regulation of cellular process developmental process multicellular organism development multicellular organismal process anterior/posterior axis specification anatomical structure development anterior/posterior pattern specification pattern specification process axis specification regionalization tissue development mesoderm development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway cellular developmental process cell differentiation cell fate commitment embryonic axis specification embryonic pattern specification embryo development head development Spemann organizer formation anatomical structure morphogenesis anatomical structure formation involved in morphogenesis developmental induction stem cell fate commitment chordate embryonic development mesenchyme development neural crest formation embryo development ending in birth or egg hatching neural crest cell fate commitment neural crest cell differentiation animal organ development epithelial to mesenchymal transition stem cell differentiation mesenchymal cell differentiation nervous system development generation of neurons neurogenesis neuron differentiation system development positive regulation of DNA-templated transcription positive regulation of biological process 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 positive regulation of cellular 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 regulation of developmental process negative regulation of cell fate specification negative regulation of biological process regulation of cell differentiation negative regulation of cell fate commitment negative regulation of cardiac cell fate specification cardiac cell fate specification negative regulation of cellular process cardiac cell fate commitment negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of cardiocyte differentiation heart development regulation of cell fate commitment negative regulation of developmental process cell fate specification cardiocyte differentiation circulatory system development regulation of cell fate specification regulation of cardiocyte differentiation regulation of cardiac cell fate specification negative regulation of multicellular organismal process	cellular anatomical structure extracellular region extracellular space
A	Frizzled-8	protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity G protein-coupled receptor activity PDZ domain binding protein domain specific binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding Wnt-protein binding	developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation T cell differentiation leukocyte differentiation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system dense core granule intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system dense core granule intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle vesicle neuronal dense core vesicle extracellular region cell periphery plasma membrane membrane protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
C	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
C	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
C	IPR000742	EGF-like domain	Domain
C	IPR000033	LDLR class B repeat	Repeat
C	IPR050778	Cueball/EGF/LRP/Nidogen	Family
C	IPR017049	Low density lipoprotein receptor-related protein 5/6	Family
C	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
B	IPR005817	Wnt	Family
B	IPR013301	Wnt-8 protein	Family
B	IPR034312	Protein Wnt-8A/8C	Family
B	IPR043158	Wnt, C-terminal domain	Homologous Superfamily
B	IPR018161	Wnt protein, conserved site	Conserved Site
A	IPR036790	Frizzled cysteine-rich domain superfamily	Homologous Superfamily
A	IPR015526	Frizzled/secreted frizzled-related protein	Family
A	IPR000539	Frizzled/Smoothened, 7TM	Domain
A	IPR041776	Frizzled 8, cysteine-rich domain	Domain
A	IPR020067	Frizzled domain	Domain
A	IPR017981	GPCR, family 2-like, 7TM	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: O75581	coronary artery disease, autosomal dominant 2 tooth agenesis, selective, 7 triple-negative breast carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor hereditary spastic paraplegia lung cancer Oligodontia Pick disease tooth agenesis adrenal cortex carcinoma malignant ependymoma osteogenesis imperfecta primitive neuroectodermal tumor astrocytic tumor coronary artery disease, autosomal dominant 2 tooth agenesis, selective, 7 triple-negative breast carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor hereditary spastic paraplegia lung cancer Oligodontia Pick disease tooth agenesis adrenal cortex carcinoma malignant ependymoma osteogenesis imperfecta primitive neuroectodermal tumor astrocytic tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma progressive supranuclear palsy

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.