Annotations: 4KNG

Crystal structure of human LGR5-RSPO1-RNF43

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)
D [auth P]	d4kngp_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Growth factor receptor domain	Growth factor receptor domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth M]	d4kngm_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Growth factor receptor domain	Growth factor receptor domain	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)
D [auth P]	SCOP2B Superfamily	Growth factor receptor domain-like	8052293	3000398	SCOP2B (2022-06-29)
C [auth M]	SCOP2B Superfamily	Growth factor receptor domain-like	8052293	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)
A		e4kngA5	A: alpha arrays	X: PH domain-like	H: PH domain-like	T: PH domain-like	F:	ECOD (v295)
B		e4kngB4	A: alpha arrays	X: PH domain-like	H: PH domain-like	T: PH domain-like	F:	ECOD (v295)
D [auth P]	Fer4_13	e4kngP2	A: alpha arrays	X: PH domain-like	H: PH domain-like	T: PH domain-like	F: Fer4_13	ECOD (v295)
C [auth M]	Fer4_13	e4kngM2	A: alpha arrays	X: PH domain-like	H: PH domain-like	T: PH domain-like	F: Fer4_13	ECOD (v295)
E	MCD_N	e4kngE1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: MCD_N	ECOD (v295)
F	MCD_N	e4kngF1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: MCD_N	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
B	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
D [auth P]	2.10.220.10	Mainly Beta	Ribbon	Hormone Receptor, Insulin-like Growth Factor Receptor 1	Chain A domain 2	CATH (4.3.0)
C [auth M]	2.10.220.10	Mainly Beta	Ribbon	Hormone Receptor, Insulin-like Growth Factor Receptor 1	Chain A domain 2	CATH (4.3.0)
E	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
F	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A, B	PF01462	Leucine rich repeat N-terminal domain (LRRNT)	Leucine rich repeat N-terminal domain	-	Family
A, B	PF12799	Leucine Rich repeats (2 copies) (LRR_4)	Leucine Rich repeats (2 copies)	-	Repeat
C [auth M], D [auth P]	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
E, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation G protein-coupled receptor signaling pathway cellular process signal transduction cell communication positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation G protein-coupled receptor signaling pathway cellular process signal transduction cell communication 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
C [auth M], D [auth P]	R-spondin-1	protein binding binding signaling receptor binding G protein-coupled receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	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 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 biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway biological regulation regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of localization import into cell regulation of cellular component organization receptor internalization regulation of transport transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport regulation of receptor internalization establishment of localization vesicle-mediated transport cellular component organization localization cellular component organization or biogenesis endocytosis receptor-mediated endocytosis regulation of endocytosis	cellular anatomical structure extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
E, F	E3 ubiquitin-protein ligase RNF43	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 cellular response to stimulus regulation of cellular process response to stimulus 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 cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication stem cell proliferation cell population proliferation receptor catabolic process receptor metabolic process Wnt receptor catabolic process 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	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane organelle subcompartment membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A, B	IPR001611	Leucine-rich repeat	Repeat
A, B	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B	IPR002131	Glycoprotein hormone receptor family	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
C [auth M], D [auth P]	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
C [auth M], D [auth P]	IPR043601	R-spondin, Fu-CRD domain	Domain
C [auth M], D [auth P]	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
C [auth M], D [auth P]	IPR051514	R-spondin domain-containing protein	Family
C [auth M], D [auth P]	IPR006212	Furin-like repeat	Repeat
C [auth M], D [auth P]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
E, F	IPR051073	ZNRF3/Arkadia E3 ubiquitin-protein ligases	Family
E, F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
E, F	IPR040700	ZNRF-3, ectodomain	Domain
E, F	IPR045907	E3 ubiquitin-protein ligase RNF43, Zinc finger, RING-type	Domain
E, F	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	: 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
C [auth M], D [auth P]	: Q2MKA7	palmoplantar keratosis Palmoplantar Hyperkeratosis with Squamous Cell Carcinoma of Skin and Sex Reversal palmoplantar keratoderma-XX sex reversal-predisposition to squamous cell carcinoma syndrome breast cancer erythrokeratoderma ovarian cancer breast carcinoma endometrial carcinoma lung adenocarcinoma ovarian carcinoma osteosarcoma
E, F	: Q68DV7	cholangiocarcinoma Liver Diseases, Parasitic prostate cancer endometrial carcinoma intrahepatic cholangiocarcinoma colorectal cancer sessile serrated polyposis cancer syndrome invasive ductal breast carcinoma lung cancer Alzheimer disease ovarian neoplasm pancreatic neoplasm colorectal carcinoma prostate carcinoma endometrial cancer cholangiocarcinoma Liver Diseases, Parasitic prostate cancer endometrial carcinoma intrahepatic cholangiocarcinoma colorectal cancer sessile serrated polyposis cancer syndrome invasive ductal breast carcinoma lung cancer Alzheimer disease ovarian neoplasm pancreatic neoplasm colorectal carcinoma prostate carcinoma endometrial cancer exocrine pancreatic carcinoma gastric neoplasm interstitial cystitis malignant colon neoplasm non-small cell lung carcinoma benign neoplasm of pancreas pancreatic intraductal papillary-mucinous carcinoma colorectal adenocarcinoma hereditary diffuse gastric adenocarcinoma lung adenocarcinoma malignant ependymoma ovarian carcinoma bile duct cancer pancreatic intraductal papillary-mucinous neoplasm ductal breast carcinoma in situ gastric cancer hypertensive disorder

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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.