8FFE | pdb_00008ffe

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	F_UNCLASSIFIED	e8ffeA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8ffeA4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth L]	F_UNCLASSIFIED	e8ffeL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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 (2025-08-29)
C [auth L]	Light Chain	IGKV1	Kappa	low-density lipoprotein receptor-related protein 6	SAbDab (2025-08-29)

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
A	Low-density lipoprotein receptor-related protein 6	protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity coreceptor activity toxin transmembrane transporter activity transporter activity transmembrane transporter activity enzyme regulator activity molecular function inhibitor activity molecular function regulator activity protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity Wnt receptor activity coreceptor activity toxin transmembrane transporter activity transporter activity transmembrane transporter activity enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity kinase inhibitor activity kinase regulator activity G protein-coupled receptor binding frizzled binding lipoprotein particle receptor activity low-density lipoprotein particle receptor activity cargo receptor activity identical protein binding protein homodimerization activity protein dimerization activity protein kinase inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity Wnt-protein binding	regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus response to sterol response to stimulus response to lipid response to alcohol regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus response to sterol response to stimulus response to lipid response to alcohol 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 response to sterol cellular response to cholesterol positive regulation of cytosolic calcium ion concentration regulation of biological quality 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 response to hormone response to endogenous stimulus response to peptide hormone response to nitrogen compound cell surface receptor signaling pathway signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway localization import into cell transport endocytosis establishment of localization vesicle-mediated transport protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane multicellular organismal process chordate embryonic development embryo development neural crest formation epithelial to mesenchymal transition multicellular organism development anatomical structure morphogenesis embryo development ending in birth or egg hatching anatomical structure formation involved in morphogenesis 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 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 positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process regulation of macromolecule metabolic process 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 head development dopaminergic neuron differentiation brain development generation of neurons neurogenesis central nervous system neuron differentiation central nervous system development neuron differentiation midbrain development midbrain dopaminergic neuron differentiation cell adhesion cell-cell adhesion transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II muscle cell apoptotic process smooth muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological 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 negative regulation of cellular process apoptotic process programmed cell death	cell surface cellular anatomical structure cell periphery plasma membrane membrane membrane microdomain membrane raft protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane protein complex Wnt signalosome membrane-bounded organelle intracellular organelle cell surface cellular anatomical structure cell periphery plasma membrane membrane membrane microdomain membrane raft protein-containing complex Wnt-Frizzled-LRP5/6 complex plasma membrane protein complex membrane protein complex 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 somatodendritic compartment cell body neuronal cell body endoplasmic reticulum
B [auth H]	YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker	-	-	-
C [auth L]	YW210.09 Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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 R01GM157729.