5BPU | pdb_00005bpu

Crystal structure of Norrin, a Wnt signalling activator, Crystal Form I

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Cys_knot	e5bpuF1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: Cys_knot	ECOD (1.6)
E	Cys_knot	e5bpuE1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: Cys_knot	ECOD (1.6)
D	Cys_knot	e5bpuD1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: Cys_knot	ECOD (1.6)
C	Cys_knot	e5bpuC1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: Cys_knot	ECOD (1.6)
B	Cys_knot	e5bpuB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: Cys_knot	ECOD (1.6)
A	Cys_knot	e5bpuA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: Cys_knot	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
E	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
D	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
C	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
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, B, C, D, E A, B, C, D, E, F	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
H [auth I]	(GGL)EEE	-	-	-
G [auth H]	(GGL)EEEEEE	-	-	-
A, B, C, D, E A, B, C, D, E, F	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 primary 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 modified amino acid metabolic process sulfur compound metabolic process amide metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-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 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 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 regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic 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 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 positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling import into cell ubiquitin-dependent endocytosis establishment of protein localization nitrogen compound transport transport establishment of localization vesicle-mediated transport localization establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle intracellular protein localization 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 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 cellular localization 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	cellular anatomical structure extracellular region extracellular space cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003064	Norrie disease protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006208	Glycoprotein hormone subunit beta	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006207	Cystine knot, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	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 R01GM157729.