4C9R | pdb_00004c9r

Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form I

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4c9rb_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Growth factor receptor domain	automated matches	automated matches	WESTERN CLAWED FROG (Xenopus tropicalis ) [TaxId: 8364 ],	SCOPe (2.08)
D	d4c9rd1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Growth factor receptor domain	automated matches	automated matches	WESTERN CLAWED FROG (Xenopus tropicalis ) [TaxId: 8364 ],	SCOPe (2.08)
D	d4c9rd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	WESTERN CLAWED FROG (Xenopus tropicalis ) [TaxId: 8364 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Furin-like repeat	8044726	4004103	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Growth factor receptor domain-like	8052294	3000398	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Growth factor receptor domain-like	8052294	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	PA_like	e4c9rA1	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)
C	PA_like	e4c9rC1	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	e4c9rB1	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)
D	Furin-like_2	e4c9rD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
C	3.50.30.30	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
B	2.10.220.10	Mainly Beta	Ribbon	Hormone Receptor, Insulin-like Growth Factor Receptor 1	Chain A domain 2	CATH (4.3.0)
D	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, 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, D	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, 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 ubiquitin-like protein ligase activity ubiquitin protein ligase activity cation binding ion binding binding metal ion binding small molecule binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein 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 developmental process multicellular organism development multicellular organismal process limb development appendage development anatomical structure development stem cell proliferation cell population proliferation receptor catabolic process receptor metabolic process 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 anterior/posterior pattern specification pattern specification process regionalization non-canonical Wnt signaling pathway regulation of non-canonical Wnt signaling pathway negative regulation of non-canonical Wnt signaling pathway	cell periphery cellular anatomical structure plasma membrane membrane
B, D	R-SPONDIN-2	protein binding binding BMP receptor binding receptor serine/threonine kinase binding signaling receptor binding transmembrane receptor protein serine/threonine kinase binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organism development multicellular organismal process dorsal/ventral pattern formation dorsal/ventral axis specification anatomical structure development pattern specification process axis specification regionalization cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process developmental process multicellular organism development multicellular organismal process dorsal/ventral pattern formation dorsal/ventral axis specification anatomical structure development pattern specification process axis specification regionalization cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular process transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway skeletal system development system development catabolic process protein catabolic process in the vacuole lysosomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process fin development limb development pectoral fin development appendage development Wnt signaling pathway medial fin development caudal fin development dorsal fin development negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication negative regulation of cellular process regulation of signaling regulation of BMP signaling pathway negative regulation of response to stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway pelvic fin development anal fin development	cellular anatomical structure extracellular region extracellular space membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR051073	ZNRF3/Arkadia E3 ubiquitin-protein ligases	Family
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR040700	ZNRF-3, ectodomain	Domain
A, C	IPR001841	Zinc finger, RING-type	Domain
B, D	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
B, D	IPR043601	R-spondin, Fu-CRD domain	Domain
B, D	IPR036383	Thrombospondin type-1 (TSP1) repeat superfamily	Homologous Superfamily
B, D	IPR051514	R-spondin domain-containing protein	Family
B, D	IPR006212	Furin-like repeat	Repeat
B, D	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B, D	IPR044004	Spondin-like TSP1 domain	Domain

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.