4F0A | pdb_00004f0a

Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Proto-oncogene Wnt3, N-terminal domain-like	8047460	4005649	SCOP2 (2022-06-29)
B	SCOP2 Family	Proto-oncogene Wnt3, C-terminal domain-like	8093189	4007801	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Serum amyloid A (SAA)-like	8093177	3002198	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Proto-oncogene Wnt3, C-terminal domain-like	8093180	3002689	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Frizzled domain-like	8034042	3001950	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)
B		e4f0aB1	A: Protein Wnt-8	X: Protein Wnt-8	H: Protein Wnt-8	T: wnt	F:	ECOD (20:10:01)
A		e4f0aA1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: Ras	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.2460.20	Alpha Beta	2-Layer Sandwich	Endo-n-acetylneuraminidase fold	Wnt (Wingless and Int-1), C-terminal domain	CATH (4.3.0)
A	1.10.2000.10	Mainly Alpha	Orthogonal Bundle	Frizzled cysteine-rich domain	Frizzled cysteine-rich domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00110	wnt family (wnt)	wnt family	-	Family
A	PF01392	Fz domain (Fz)	Fz domain	Also known as the CRD (cysteine rich domain), the C6 box in MuSK receptor. This domain of unknown function has been independently identified by several groups [1,2,3,4]. The domain contains 10 conserved cysteines.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Protein Wnt-8	molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein binding binding enzyme binding protease binding signaling receptor binding G protein-coupled receptor binding frizzled binding	developmental process multicellular organism development multicellular organismal process anterior/posterior axis specification anatomical structure development anterior/posterior pattern specification pattern specification process axis specification regionalization tissue development mesoderm development cellular response to stimulus regulation of biological process regulation of cellular process developmental process multicellular organism development multicellular organismal process anterior/posterior axis specification anatomical structure development anterior/posterior pattern specification pattern specification process axis specification regionalization tissue development mesoderm development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway cellular developmental process cell differentiation cell fate commitment embryonic axis specification embryonic pattern specification embryo development Spemann organizer formation anatomical structure morphogenesis anatomical structure formation involved in morphogenesis developmental induction stem cell fate commitment chordate embryonic development mesenchyme development neural crest formation embryo development ending in birth or egg hatching neural crest cell fate commitment neural crest cell differentiation animal organ development epithelial to mesenchymal transition stem cell differentiation mesenchymal cell differentiation nervous system development generation of neurons neurogenesis neuron differentiation system development 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 primary metabolic process 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 metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of developmental process negative regulation of cell fate specification negative regulation of biological process regulation of cell differentiation negative regulation of cell fate commitment negative regulation of cardiac cell fate specification cardiac cell fate specification negative regulation of cellular process cardiac cell fate commitment negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of cardiocyte differentiation heart development regulation of cell fate commitment negative regulation of developmental process cell fate specification cardiocyte differentiation circulatory system development regulation of cell fate specification regulation of cardiocyte differentiation regulation of cardiac cell fate specification negative regulation of multicellular organismal process	cellular anatomical structure extracellular region cell periphery extracellular matrix external encapsulating structure extracellular space
A	Frizzled-8	protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity G protein-coupled receptor activity PDZ domain binding protein domain specific binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding Wnt-protein binding	developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway non-canonical Wnt signaling pathway cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation T cell differentiation leukocyte differentiation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system dense core granule intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system dense core granule intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle vesicle neuronal dense core vesicle extracellular region cell periphery plasma membrane membrane protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR005817	Wnt	Family
B	IPR013301	Wnt-8 protein	Family
B	IPR034312	Protein Wnt-8A/8C	Family
B	IPR043158	Wnt, C-terminal domain	Homologous Superfamily
B	IPR018161	Wnt protein, conserved site	Conserved Site
A	IPR036790	Frizzled cysteine-rich domain superfamily	Homologous Superfamily
A	IPR015526	Frizzled/secreted frizzled-related protein	Family
A	IPR000539	Frizzled/Smoothened, 7TM	Domain
A	IPR041776	Frizzled 8, cysteine-rich domain	Domain
A	IPR020067	Frizzled domain	Domain
A	IPR017981	GPCR, family 2-like, 7TM	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.