4UFS | pdb_00004ufs

Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5 and ZNRF3

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	Growth factor receptor domain-like	8052292	3000398	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	PA_like	e4ufsC1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PA_like	ECOD (1.6)
B	Furin-like_2	e4ufsB1	A: few secondary structure elements	X: EGF-like	H: Growth factor receptor domain (From Topology)	T: Growth factor receptor domain	F: Furin-like_2	ECOD (1.6)
A	LRR_8_3	e4ufsA1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF18212	ZNRF-3 Ectodomain (ZNRF_3_ecto)	ZNRF-3 Ectodomain	This domain is found in ZNRF-3 protein present in Danio rerio. ZNRF-3 is a transmembrane E3 ubiquitin ligase that antagonizes Wnt signalling, the signalling system used to mediate Rspo protein actions. ZNFR3 and RNF43, alongside the Rspo proteins, ha ...	This domain is found in ZNRF-3 protein present in Danio rerio. ZNRF-3 is a transmembrane E3 ubiquitin ligase that antagonizes Wnt signalling, the signalling system used to mediate Rspo protein actions. ZNFR3 and RNF43, alongside the Rspo proteins, have emerged as a system with therapeutic potential for a number of pathological processes. This domain is known as the ectodomain [1].	Domain
B	PF15913	Furin-like repeat, cysteine-rich (Furin-like_2)	Furin-like repeat, cysteine-rich	The furin-like cysteine rich region has been found in a variety of proteins from eukaryotes that are involved in the mechanism of signal transduction by receptor tyrosine kinases, which involves receptor aggregation.	Domain
A	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A	PF01462	Leucine rich repeat N-terminal domain (LRRNT)	Leucine rich repeat N-terminal domain	-	Family
A	PF12799	Leucine Rich repeats (2 copies) (LRR_4)	Leucine Rich repeats (2 copies)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein binding signaling receptor binding G protein-coupled receptor binding frizzled binding	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process developmental process multicellular organism development multicellular organismal process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process developmental process multicellular organism development multicellular organismal process limb development appendage development anatomical structure development stem cell proliferation cell population proliferation regulation of Wnt signaling pathway, planar cell polarity pathway cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process regulation of Wnt signaling pathway cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction Wnt signaling pathway, planar cell polarity pathway regulation of non-canonical Wnt signaling pathway cell communication regulation of response to stimulus regulation of cell communication non-canonical Wnt signaling pathway signal transduction Wnt signaling pathway receptor catabolic process negative regulation of signaling negative regulation of biological process negative regulation of cell communication negative regulation of Wnt signaling pathway receptor metabolic process negative regulation of cellular process negative regulation of response to stimulus negative regulation of signal transduction Wnt receptor catabolic process regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of canonical Wnt signaling pathway protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal negative regulation of non-canonical Wnt signaling pathway	cell periphery cellular anatomical structure plasma membrane membrane
B	R-SPONDIN-2	protein binding binding signaling receptor binding BMP receptor binding receptor serine/threonine kinase binding transmembrane receptor protein serine/threonine kinase binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organismal process regulation of biological process regulation of animal organ morphogenesis regulation of developmental process regulation of odontogenesis of dentin-containing tooth negative regulation of developmental process regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis animal organ development biological regulation negative regulation of biological process negative regulation of odontogenesis anatomical structure morphogenesis developmental process multicellular organismal process regulation of biological process regulation of animal organ morphogenesis regulation of developmental process regulation of odontogenesis of dentin-containing tooth negative regulation of developmental process regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis animal organ development biological regulation negative regulation of biological process negative regulation of odontogenesis anatomical structure morphogenesis negative regulation of odontogenesis of dentin-containing tooth anatomical structure development animal organ morphogenesis negative regulation of animal organ morphogenesis regulation of multicellular organismal process negative regulation of multicellular organismal process regulation of anatomical structure morphogenesis cellular developmental process ossification cell differentiation cellular process osteoblast differentiation lung growth developmental growth tube development growth respiratory tube development organ growth multicellular organism development lung development respiratory system development system development trachea cartilage morphogenesis connective tissue development trachea cartilage development trachea morphogenesis tissue development tissue morphogenesis skeletal system development trachea development cartilage morphogenesis cartilage development limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development forelimb morphogenesis appendage morphogenesis limb morphogenesis bone mineralization biomineral tissue development branching morphogenesis of an epithelial tube tube morphogenesis lung morphogenesis epithelial tube morphogenesis epithelium development morphogenesis of an epithelium morphogenesis of a branching structure epithelial tube branching involved in lung morphogenesis morphogenesis of a branching epithelium embryonic hindlimb morphogenesis hindlimb morphogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of canonical Wnt signaling pathway dopaminergic neuron differentiation nervous system development generation of neurons neurogenesis neuron differentiation	cell surface cellular anatomical structure extracellular region extracellular space
A	LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5	molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity protein-hormone receptor activity	developmental process multicellular organismal process epithelium development cell population proliferation tube development morphogenesis of an epithelium tissue development renal system development epithelial cell proliferation involved in renal tubule morphogenesis tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure development renal tubule development developmental process multicellular organismal process epithelium development cell population proliferation tube development morphogenesis of an epithelium tissue development renal system development epithelial cell proliferation involved in renal tubule morphogenesis tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure development renal tubule development cellular process epithelial tube morphogenesis epithelial cell proliferation renal tubule morphogenesis system development sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation cell differentiation germ cell development oocyte differentiation ear development sensory organ development inner ear development animal organ development regulation of biological process regulation of cellular process regulation of cell population proliferation biological regulation cellular response to stimulus response to stimulus signaling G protein-coupled receptor signaling pathway signal transduction cell communication epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of cellular process positive regulation of canonical Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment membrane trans-Golgi network membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment membrane trans-Golgi network membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm organelle membrane cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR051073	ZNRF3/Arkadia E3 ubiquitin-protein ligases	Family
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR040700	ZNRF-3, ectodomain	Domain
C	IPR045903	E3 ubiquitin-protein ligase ZNRF3, zinc finger, RING-type	Domain
C	IPR001841	Zinc finger, RING-type	Domain
B	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
B	IPR043601	R-spondin, Fu-CRD domain	Domain
B	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
B	IPR051514	R-spondin domain-containing protein	Family
B	IPR006212	Furin-like repeat	Repeat
B	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B	IPR044004	Spondin-like TSP1 domain	Domain
A	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A	IPR001611	Leucine-rich repeat	Repeat
A	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR002131	Glycoprotein hormone receptor family	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q9ULT6	adrenal cortex carcinoma pancreatic neoplasm subependymal giant cell astrocytoma adrenal carcinoma colorectal adenocarcinoma interstitial cystitis malignant ependymoma medulloblastoma open-angle glaucoma pancreatic intraductal papillary-mucinous carcinoma Pick disease exocrine pancreatic carcinoma lung adenocarcinoma Malignant neoplasm of pancreas nasopharyngeal carcinoma adrenal cortex carcinoma pancreatic neoplasm subependymal giant cell astrocytoma adrenal carcinoma colorectal adenocarcinoma interstitial cystitis malignant ependymoma medulloblastoma open-angle glaucoma pancreatic intraductal papillary-mucinous carcinoma Pick disease exocrine pancreatic carcinoma lung adenocarcinoma Malignant neoplasm of pancreas nasopharyngeal carcinoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia squamous cell carcinoma carcinoma of esophagus gastric carcinoma lung carcinoma malignant pancreatic neoplasm non-alcoholic fatty liver disease ovarian cancer
A	Pharos: O75473	malignant colon neoplasm colorectal cancer nasopharyngeal carcinoma Pick disease Sjogren syndrome atopic eczema colonic neoplasm Colorectal Neoplasms digestive system disease large cell medulloblastoma lung carcinoma malignant pancreatic neoplasm ovarian cancer progressive supranuclear palsy benign colon neoplasm malignant colon neoplasm colorectal cancer nasopharyngeal carcinoma Pick disease Sjogren syndrome atopic eczema colonic neoplasm Colorectal Neoplasms digestive system disease large cell medulloblastoma lung carcinoma malignant pancreatic neoplasm ovarian cancer progressive supranuclear palsy benign colon neoplasm cutaneous lupus erythematosus Duchenne muscular dystrophy limb-girdle muscular dystrophy medulloblastoma pancreatic intraductal papillary-mucinous neoplasm psoriasis cancer colorectal carcinoma cystic fibrosis head and neck cancer lung cancer malignant ependymoma

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.