4QXF

crystal structure of human LGR4 and Rspo1

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 C]	d4qxfc_	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 E]	d4qxfe_	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 C]	SCOP2B Superfamily	Growth factor receptor domain-like	8052293	3000398	SCOP2B (2022-06-29)
C [auth E]	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	PF11921,PF13855	e4qxfA1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: PF11921,PF13855	ECOD (1.6)
B	PF11921,PF13855	e4qxfB1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: PF11921,PF13855	ECOD (1.6)
D [auth C]	PF15913	e4qxfC1	A: few secondary structure elements	X: EGF-like	H: Growth factor receptor domain (From Topology)	T: Growth factor receptor domain	F: PF15913	ECOD (1.6)
C [auth E]	PF15913	e4qxfE1	A: few secondary structure elements	X: EGF-like	H: Growth factor receptor domain (From Topology)	T: Growth factor receptor domain	F: PF15913	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	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 E]	2.10.220.10	Mainly Beta	Ribbon	Hormone Receptor, Insulin-like Growth Factor Receptor 1	Chain A domain 2	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	PF11921	Domain of unknown function (DUF3439) (DUF3439)	Domain of unknown function (DUF3439)	-	Family
C [auth E], D [auth C]	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

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 4, Variable lymphocyte receptor B	molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity peptide receptor activity G protein-coupled peptide receptor activity protein-hormone receptor activity	multicellular organismal process tissue remodeling bone remodeling regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process multicellular organismal process tissue remodeling bone remodeling regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process developmental 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 epithelial tube morphogenesis epithelial cell proliferation renal tubule morphogenesis system development cellular developmental process ossification cell differentiation osteoblast differentiation cellular response to stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to stimulus toll-like receptor signaling pathway regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response regulation of toll-like receptor signaling pathway activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus signaling negative regulation of signaling positive regulation of biological process negative regulation of cell communication positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus defense response to symbiont negative regulation of signal transduction negative regulation of toll-like receptor signaling pathway negative regulation of immune system process immune system process regulation of cell communication spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation bone mineralization animal organ development biomineral tissue development mesonephric epithelium development kidney epithelium development branching morphogenesis of an epithelial tube nephron tubule morphogenesis regulation of kidney development regulation of branching involved in ureteric bud morphogenesis positive regulation of developmental process animal organ morphogenesis nephron development regulation of morphogenesis of a branching structure regulation of animal organ morphogenesis positive regulation of multicellular organismal process mesonephric tubule development regulation of developmental process nephron morphogenesis nephron epithelium morphogenesis nephron tubule development ureteric bud morphogenesis positive regulation of morphogenesis of an epithelium branching involved in ureteric bud morphogenesis regulation of morphogenesis of an epithelium regulation of multicellular organismal process regulation of anatomical structure morphogenesis nephron epithelium development ureteric bud development mesonephros development kidney morphogenesis morphogenesis of a branching structure positive regulation of branching involved in ureteric bud morphogenesis mesonephric tubule morphogenesis kidney development morphogenesis of a branching epithelium digestive system development digestive tract development epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process genitalia development reproductive system development sex differentiation male sex differentiation male genitalia development reproductive structure development multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells intestinal stem cell homeostasis rhythmic process circadian regulation of gene expression circadian rhythm adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cytokine production regulation of cytokine production negative regulation of cytokine production negative regulation of gene expression negative regulation of multicellular organismal process cell differentiation involved in metanephros development cell differentiation involved in kidney development metanephros development metanephric tubule morphogenesis metanephric epithelium development metanephros morphogenesis metanephric nephron tubule morphogenesis metanephric nephron development metanephric nephron epithelium development metanephric nephron tubule development metanephric nephron morphogenesis metanephric tubule development 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 cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway positive regulation of signaling negative regulation of cold-induced thermogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis metanephric glomerulus development glomerulus development	membrane cellular anatomical entity cell periphery plasma membrane
C [auth E], D [auth C]	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 cellular metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process 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	extracellular region cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A, B	IPR024592	Variable lymphocyte receptor, C-terminal	Domain
A, B	IPR001611	Leucine-rich repeat	Repeat
A, B	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, B	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A, B	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR002131	Glycoprotein hormone receptor family	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR001611	Leucine-rich repeat	Repeat
A, B	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C [auth E], D [auth C]	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
C [auth E], D [auth C]	IPR043601	R-spondin, Fu-CRD domain	Domain
C [auth E], D [auth C]	IPR036383	Thrombospondin type-1 (TSP1) repeat superfamily	Homologous Superfamily
C [auth E], D [auth C]	IPR006212	Furin-like repeat	Repeat
C [auth E], D [auth C]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9BXB1	BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 17 adenoma glioblastoma lung adenocarcinoma malignant glioma obesity disorder psoriasis adrenal cortex carcinoma breast cancer interstitial cystitis lung cancer malignant mesothelioma osteoporosis spina bifida atypical teratoid rhabdoid tumor BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 17 adenoma glioblastoma lung adenocarcinoma malignant glioma obesity disorder psoriasis adrenal cortex carcinoma breast cancer interstitial cystitis lung cancer malignant mesothelioma osteoporosis spina bifida atypical teratoid rhabdoid tumor breast carcinoma large cell medulloblastoma lung carcinoma non-small cell lung carcinoma osteosarcoma
C [auth E], D [auth C]	Pharos: 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

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.