6BD4

Crystal structure of human apo-Frizzled4 receptor

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Class F (frizzled) G protein-coupled receptor-like	8091113	4006379	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	G protein-coupled receptor-like	8091114	3000473	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Rubredoxin-like	8039183	3001257	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	Frizzled	e6bd4A2	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Frizzled	ECOD (1.6)
A	Rubredoxin	e6bd4A1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Rubredoxin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.28.10	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00301	Rubredoxin (Rubredoxin)	Rubredoxin	-	Domain
A	PF01534	Frizzled/Smoothened family membrane region (Frizzled)	Frizzled/Smoothened family membrane region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Frizzled-4/Rubredoxin chimeric protein	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity amide binding amyloid-beta binding binding peptide binding protein-containing complex binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding Wnt-protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity amide binding amyloid-beta binding binding peptide binding protein-containing complex binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding Wnt-protein binding G protein-coupled receptor activity PDZ domain binding protein domain specific binding protein heterodimerization activity protein dimerization activity cytokine receptor activity immune receptor activity cytokine binding identical protein binding protein homodimerization activity electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	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 cell population proliferation cell adhesion 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 cell population proliferation cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion positive regulation of DNA-binding transcription factor activity cellular biosynthetic process RNA metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular aromatic compound metabolic process response to organic substance response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid response to chemical cellular response to lipid cellular response to organic substance multicellular organismal process system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process cellular developmental process regulation of neuron projection arborization cell projection organization plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development neuron projection development cell morphogenesis regulation of cell morphogenesis cellular component organization positive regulation of developmental process neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization cellular component organization or biogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization positive regulation of neuron projection arborization nervous system development generation of neurons anatomical structure morphogenesis neuron projection arborization neuron development sensory organ development blood vessel morphogenesis tube development retina vasculature development in camera-type eye eye development animal organ development retina development in camera-type eye visual system development retina vasculature morphogenesis in camera-type eye vasculature development circulatory system development tube morphogenesis camera-type eye development retinal blood vessel morphogenesis sensory system development blood vessel development establishment of blood-brain barrier central nervous system development angiogenesis anatomical structure formation involved in morphogenesis head development cerebellum vasculature development brain development cerebellum development metencephalon development cerebellum vasculature morphogenesis hindbrain development non-canonical Wnt signaling pathway epithelium development endothelial cell differentiation endothelium development tissue development epithelial cell differentiation Norrin signaling pathway cellular process involved in reproduction in multicellular organism localization development of primary sexual characteristics reproductive structure development regulation of biological quality gonad development luteinization regulation of hormone levels organic substance transport lipid transport establishment of localization endocrine hormone secretion lipid export from cell ovulation cycle process transport reproductive process steroid hormone secretion sex differentiation development of primary female sexual characteristics hormone secretion developmental process involved in reproduction progesterone secretion ovulation cycle secretion by cell signal release rhythmic process reproductive system development secretion female gonad development multicellular organismal reproductive process lipid localization export from cell cell-cell signaling female sex differentiation endocrine process macromolecule localization hormone transport cellular response to growth factor stimulus regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway regulation of signaling response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway regulation of response to stimulus regulation of cell communication response to growth factor vasculogenesis positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion extracellular matrix-cell signaling regulation of cell-substrate adhesion regulation of cell adhesion negative regulation of biological process negative regulation of cell adhesion negative regulation of cellular process negative regulation of cell-substrate adhesion Wnt signaling pathway, calcium modulating pathway positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of nitrogen compound metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process behavior locomotory behavior locomotion involved in locomotory behavior positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of dendrite morphogenesis positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development regulation of nervous system development positive regulation of cell differentiation dendrite development positive regulation of neurogenesis regulation of multicellular organismal process regulation of multicellular organismal development positive regulation of dendrite morphogenesis dendrite morphogenesis cell morphogenesis involved in neuron differentiation regulation of plasma membrane bounded cell projection organization response to cytokine response to leukemia inhibitory factor cellular response to leukemia inhibitory factor cellular response to cytokine stimulus	cell-cell junction anchoring junction cell junction cellular anatomical entity membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle cell-cell junction anchoring junction cell junction cellular anatomical entity membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse glutamatergic synapse cell surface cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036790	Frizzled cysteine-rich domain superfamily	Homologous Superfamily
A	IPR041765	Frizzled 4, cysteine-rich domain	Domain
A	IPR017981	GPCR, family 2-like, 7TM	Domain
A	IPR000539	Frizzled/Smoothened, 7TM	Domain
A	IPR020067	Frizzled domain	Domain
A	IPR015526	Frizzled/secreted frizzled-related protein	Family
A	IPR026551	Frizzled-4, 7TM	Domain
A	IPR018527	Rubredoxin, iron-binding site	Binding Site
A	IPR024922	Rubredoxin	Family
A	IPR024934	Rubredoxin-like domain	Domain
A	IPR024935	Rubredoxin domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9ULV1	exudative vitreoretinopathy 1 retinopathy of prematurity persistent hyperplastic primary vitreous cleft palate exudative vitreoretinopathy Arachnodactyly retinal disease syndactyly non-syndromic syndactyly pancreatic intraductal papillary-mucinous neoplasm psoriasis breast fibroadenoma lung adenocarcinoma major affective disorder 2 Norrie disease exudative vitreoretinopathy 1 retinopathy of prematurity persistent hyperplastic primary vitreous cleft palate exudative vitreoretinopathy Arachnodactyly retinal disease syndactyly non-syndromic syndactyly pancreatic intraductal papillary-mucinous neoplasm psoriasis breast fibroadenoma lung adenocarcinoma major affective disorder 2 Norrie disease bipolar disorder cataract Coats disease ductal breast carcinoma in situ lung cancer non-small cell lung carcinoma osteosarcoma polysyndactyly 4 breast carcinoma colorectal cancer invasive ductal breast carcinoma lung carcinoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	Frizzled/Smoothened family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class F	Frizzled 4 (FZD4) receptor in the ligand-free state

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.