8FFE

Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00058	e8ffeA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF00058	ECOD (1.6)
A	PF14670	e8ffeA4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF14670	ECOD (1.6)
C [auth L]	PF07654	e8ffeL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e8ffeL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV3	-	low-density lipoprotein receptor-related protein 6	SAbDab (2024-08-09)
C [auth L]	Light Chain	IGKV1	Kappa	low-density lipoprotein receptor-related protein 6	SAbDab (2024-08-09)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain
A	PF00058	Low-density lipoprotein receptor repeat class B (Ldl_recept_b)	Low-density lipoprotein receptor repeat class B	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker	-	-	-
A	Low-density lipoprotein receptor-related protein 6	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity coreceptor activity enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity kinase inhibitor activity kinase regulator activity protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity coreceptor activity enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity kinase inhibitor activity kinase regulator activity protein binding binding signaling receptor binding G protein-coupled receptor binding frizzled binding identical protein binding Wnt-protein binding toxin transmembrane transporter activity transporter activity transmembrane transporter activity lipoprotein particle receptor activity low-density lipoprotein particle receptor activity cargo receptor activity protein homodimerization activity protein dimerization activity	cellular response to stimulus response to sterol response to stimulus response to lipid response to alcohol cellular response to organic cyclic compound response to oxygen-containing compound response to cholesterol cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to lipid cellular process cellular response to stimulus response to sterol response to stimulus response to lipid response to alcohol cellular response to organic cyclic compound response to oxygen-containing compound response to cholesterol cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to lipid cellular process cellular response to sterol cellular response to cholesterol response to organic cyclic compound developmental process neural crest cell differentiation cellular developmental process animal organ development mesenchyme development tissue development stem cell differentiation cell differentiation anatomical structure development mesenchymal cell differentiation regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling canonical Wnt signaling pathway biological regulation cell communication signal transduction Wnt signaling pathway positive regulation of DNA-binding transcription factor activity cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane multicellular organism development multicellular organismal process nervous system development system development trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cytosolic calcium ion concentration regulation of biological quality response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to nitrogen compound import into cell transport endocytosis establishment of localization vesicle-mediated transport chordate embryonic development embryo development neural crest formation epithelial to mesenchymal transition anatomical structure morphogenesis embryo development ending in birth or egg hatching anatomical structure formation involved in morphogenesis regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of transferase activity negative regulation of cellular metabolic process negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process regulation of kinase activity negative regulation of protein phosphorylation macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of protein serine/threonine kinase activity negative regulation of cellular process protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process negative regulation of molecular function negative regulation of protein kinase activity regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation head development dopaminergic neuron differentiation brain development generation of neurons neurogenesis central nervous system development neuron differentiation midbrain development midbrain dopaminergic neuron differentiation cell adhesion cell-cell adhesion muscle cell apoptotic process smooth muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death regulation of smooth muscle cell apoptotic process negative regulation of smooth muscle cell apoptotic process negative regulation of apoptotic process negative regulation of muscle cell apoptotic process apoptotic process programmed cell death	cell periphery protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity somatodendritic compartment cell body neuronal cell body cell surface membrane microdomain membrane raft cell periphery protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity somatodendritic compartment cell body neuronal cell body cell surface membrane microdomain membrane raft Wnt signalosome membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle extracellular region endosome membrane early endosome endosome early endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane synapse cell junction endoplasmic reticulum
C [auth L]	YW210.09 Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A	IPR000033	LDLR class B repeat	Repeat
A	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
A	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A	IPR000742	EGF-like domain	Domain
A	IPR050778	Cueball/EGF/LRP/Nidogen	Family
A	IPR017049	Low density lipoprotein receptor-related protein 5/6	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75581	coronary artery disease, autosomal dominant 2 tooth agenesis, selective, 7 triple-negative breast carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor hereditary spastic paraplegia lung cancer Oligodontia Pick disease tooth agenesis adrenal cortex carcinoma malignant ependymoma osteogenesis imperfecta primitive neuroectodermal tumor astrocytic tumor coronary artery disease, autosomal dominant 2 tooth agenesis, selective, 7 triple-negative breast carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor hereditary spastic paraplegia lung cancer Oligodontia Pick disease tooth agenesis adrenal cortex carcinoma malignant ependymoma osteogenesis imperfecta primitive neuroectodermal tumor astrocytic tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma progressive supranuclear palsy

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.