5BQC

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate

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)
A [auth B]	d5bqcb_	All alpha proteins	Frizzled cysteine-rich domain	Frizzled cysteine-rich domain	automated matches	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)
A [auth B]	SCOP2B Superfamily	Frizzled domain-like	8083836	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)
A [auth B]	PF01392	e5bqcB1	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: PF01392	ECOD (1.6)
B [auth A]	PF00007	e5bqcA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00007	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.10.2000.10	Mainly Alpha	Orthogonal Bundle	Frizzled cysteine-rich domain	Frizzled cysteine-rich domain	CATH (4.3.0)
B [auth A]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	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
B [auth A]	PF00007	Cystine-knot domain (Cys_knot)	Cystine-knot domain	The family comprises glycoprotein hormones and the C-terminal domain of various extracellular proteins. It is believed to be involved in disulfide-linked dimerisation.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Frizzled-4	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	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 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 organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound 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 organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of 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 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
B [auth A]	Norrin	protein binding binding signaling receptor binding G protein-coupled receptor binding frizzled binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	developmental process multicellular organism development multicellular organismal process nerve development cranial nerve development anatomical structure development optic nerve development nervous system development system development response to stimulus response to stress response to wounding response to axon injury behavior developmental process multicellular organism development multicellular organismal process nerve development cranial nerve development anatomical structure development optic nerve development nervous system development system development response to stimulus response to stress response to wounding response to axon injury behavior exploration behavior cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway sensory organ development eye development animal organ development visual system development camera-type eye development sensory system development lens development in camera-type eye response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to chemical response to oxygen levels response to abiotic stimulus epithelium development retinal pigment epithelium development retina development in camera-type eye tissue development organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal glutathione metabolic process cellular metabolic process sulfur compound metabolic process amide metabolic process cellular modified amino acid metabolic process serine family amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process small molecule metabolic process dendritic spine development plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development cellular component organization generation of neurons neurogenesis neuron differentiation dendrite development cell differentiation neuron development cellular component organization or biogenesis cell cycle re-entry into mitotic cell cycle cell cycle process blood vessel morphogenesis tube development retina vasculature development in camera-type eye retina vasculature morphogenesis in camera-type eye vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis retinal blood vessel morphogenesis blood vessel development cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to transforming growth factor beta stimulus response to endogenous stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway enzyme-linked receptor protein signaling pathway mitotic cell cycle smoothened signaling pathway establishment of blood-brain barrier central nervous system development angiogenesis anatomical structure formation involved in morphogenesis intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction cellular biosynthetic process RNA 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 organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process action potential regulation of biological quality regulation of membrane potential axonogenesis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance retinal ganglion cell axon guidance protein localization import into cell ubiquitin-dependent endocytosis establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization vesicle-mediated transport localization establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle endocytosis endothelial cell differentiation endothelium development epithelial cell differentiation myeloid leukocyte differentiation hemopoiesis macrophage differentiation mononuclear cell differentiation gliogenesis glial cell differentiation myeloid cell differentiation microglia differentiation leukocyte differentiation aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds generation of precursor metabolites and energy establishment of blood-retinal barrier Norrin signaling pathway blood vessel remodeling tissue remodeling neuron apoptotic process apoptotic process cell death programmed cell death photoreceptor cell differentiation neural retina development eye morphogenesis eye photoreceptor cell differentiation animal organ morphogenesis camera-type eye morphogenesis camera-type eye photoreceptor cell differentiation retina morphogenesis in camera-type eye sensory organ morphogenesis retinal rod cell differentiation cone retinal bipolar cell differentiation retinal bipolar neuron differentiation glutamatergic neuron differentiation multi-multicellular organism process placenta development reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process developmental process involved in reproduction maternal placenta development female pregnancy multi-organism reproductive process decidualization extracellular matrix-cell signaling positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process sensory perception of light stimulus system process sensory perception nervous system process visual perception microglial cell proliferation cell population proliferation leukocyte proliferation macrophage proliferation glial cell proliferation protein targeting establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome establishment of localization in cell protein targeting to vacuole intracellular transport protein localization to vacuole protein localization to lysosome vacuolar transport intracellular protein transport defense response inflammatory response retina layer formation multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis retina blood vessel maintenance tissue homeostasis retina homeostasis organelle organization vacuole organization	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular region extracellular space cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR036790	Frizzled cysteine-rich domain superfamily	Homologous Superfamily
A [auth B]	IPR041765	Frizzled 4, cysteine-rich domain	Domain
A [auth B]	IPR017981	GPCR, family 2-like, 7TM	Domain
A [auth B]	IPR000539	Frizzled/Smoothened, 7TM	Domain
A [auth B]	IPR020067	Frizzled domain	Domain
A [auth B]	IPR015526	Frizzled/secreted frizzled-related protein	Family
A [auth B]	IPR026551	Frizzled-4, 7TM	Domain
B [auth A]	IPR003064	Norrie disease protein	Family
B [auth A]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
B [auth A]	IPR006208	Glycoprotein hormone subunit beta	Domain
B [auth A]	IPR006207	Cystine knot, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	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
B [auth A]	Pharos: Q00604	Norrie disease exudative vitreoretinopathy Coats disease exudative vitreoretinopathy 2, X-linked persistent hyperplastic primary vitreous retinopathy of prematurity exudative vitreoretinopathy 1 adrenal cortex carcinoma intellectual disability Retinal Nonattachment, Nonsyndromic Congenital subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor large cell medulloblastoma cataract medulloblastoma Norrie disease exudative vitreoretinopathy Coats disease exudative vitreoretinopathy 2, X-linked persistent hyperplastic primary vitreous retinopathy of prematurity exudative vitreoretinopathy 1 adrenal cortex carcinoma intellectual disability Retinal Nonattachment, Nonsyndromic Congenital subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor large cell medulloblastoma cataract medulloblastoma primitive neuroectodermal tumor schizophrenia

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 R01GM133198.