3S2K | pdb_00003s2k

Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	DIKK1-2-4_C-subdom1	e3s2kC1	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: DIKK1-2-4_C-subdom1	ECOD (v294.1)
C	EGF	e3s2kC2	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: EGF	ECOD (v294.1)
B	Pkinase, APH	e3s2kB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)
B	HORMA	e3s2kB5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: HORMA	ECOD (v294.1)
A	PIN	e3s2kA1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: HIT-related	T: HIT-related	F: PIN	ECOD (v294.1)
A	FXa_inhibition	e3s2kA8	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: PreATP-grasp domain	F: FXa_inhibition	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.10.80.10	Mainly Beta	Ribbon	Lipase, subunit A	Lipase, subunit A	CATH (4.3.0)
B	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
A	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF21481	Dickkopf-related protein 1/2/4, C-terminal subdomain 1 (DIKK1-2-4_C-subdom1)	Dickkopf-related protein 1/2/4, C-terminal subdomain 1	Dickkopf-related proteins are cysteine-rich secretory proteins and highly conserved inhibitors of the canonical Wnt signaling pathway, which play key roles in many essential biological processes. This entry represents the C-terminal cysteine-rich dom ...	Dickkopf-related proteins are cysteine-rich secretory proteins and highly conserved inhibitors of the canonical Wnt signaling pathway, which play key roles in many essential biological processes. This entry represents the C-terminal cysteine-rich domain which is strongly conserved in Dkk1, Dkk2 and Dkk4, and directly contacts LRP6 [1-4]. This domain is described as two subdomains, each consisting of three anti-parallel beta-strands that are connected by a long loop which contains a short alpha-helix. This entry represents the first subdomain, the second is covered in Pfam:PF21479. In Dkk3 the residues differ and is consistent with studies indicating that Dkk3 is a divergent family member that does not inhibit Wnt signalling [4]. This domain share significant sequence similarity to the colipase fold.	Domain
C	PF21479	Dickkopf-related protein 1/2/4, C-terminal subdomain 2 (DIKK1-2-4_C-subdom2)	Dickkopf-related protein 1/2/4, C-terminal subdomain 2	Dickkopf-related proteins are cysteine-rich secretory proteins and highly conserved inhibitors of the canonical Wnt signaling pathway, which play key roles in many essential biological processes. The C-terminal domain is described as two subdomains, ...	Dickkopf-related proteins are cysteine-rich secretory proteins and highly conserved inhibitors of the canonical Wnt signaling pathway, which play key roles in many essential biological processes. The C-terminal domain is described as two subdomains, each consisting of three anti-parallel beta-strands that are connected by a long loop which contains a short alpha-helix. This domain is strongly conserved in Dkk1, Dkk2 and Dkk4, and directly contacts LRP6. This entry represents the second subdomain [1-4]. In Dkk3 these residues differ and is consistent with studies indicating that Dkk3 is a divergent family member that does not inhibit Wnt signalling [4]. This domain share significant sequence similarity to the colipase fold.	Domain
A, B	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, B	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
C	Dickkopf-related protein 1	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity molecular function inhibitor activity signaling receptor inhibitor activity receptor antagonist activity co-receptor binding protein binding binding low-density lipoprotein particle receptor binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity molecular function inhibitor activity signaling receptor inhibitor activity receptor antagonist activity co-receptor binding protein binding binding low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process positive regulation of biological process regulation of midbrain dopaminergic neuron differentiation regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process neurogenesis multicellular organism development central nervous system neuron differentiation neuron differentiation positive regulation of cell differentiation cell differentiation multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process positive regulation of biological process regulation of midbrain dopaminergic neuron differentiation regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process neurogenesis multicellular organism development central nervous system neuron differentiation neuron differentiation positive regulation of cell differentiation cell differentiation regulation of dopaminergic neuron differentiation anatomical structure development positive regulation of cellular process system development developmental process regulation of biological process head development dopaminergic neuron differentiation biological regulation animal organ development positive regulation of dopaminergic neuron differentiation brain development nervous system development positive regulation of midbrain dopaminergic neuron differentiation generation of neurons central nervous system development midbrain development cellular process midbrain dopaminergic neuron differentiation regulation of neuron differentiation negative regulation of biological process negative regulation of muscle cell differentiation regulation of striated muscle cell differentiation regulation of cardiac muscle cell differentiation muscle cell differentiation striated muscle tissue development muscle structure development negative regulation of cardiac muscle cell differentiation negative regulation of cellular process negative regulation of cell differentiation regulation of multicellular organismal process muscle tissue development negative regulation of cardiocyte differentiation heart development cardiac muscle tissue development negative regulation of developmental process negative regulation of striated muscle cell differentiation cardiac muscle cell differentiation tissue development cardiocyte differentiation circulatory system development regulation of muscle cell differentiation regulation of cardiocyte differentiation striated muscle cell differentiation negative regulation of multicellular organismal process cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of signaling regulation of canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of cell communication positive regulation of signal transduction Wnt signaling pathway, planar cell polarity pathway positive regulation of response to stimulus positive regulation of non-canonical Wnt signaling pathway positive regulation of Wnt signaling pathway non-canonical Wnt signaling pathway positive regulation of Wnt signaling pathway, planar cell polarity pathway regulation of Wnt signaling pathway, planar cell polarity pathway regulation of non-canonical Wnt signaling pathway positive regulation of signaling cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of neuron projection development regulation of cellular component organization cell projection organization cell development neuron projection development cellular component organization cellular component organization or biogenesis negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of neuron projection development neuron development regulation of plasma membrane bounded cell projection organization negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette SMAD protein signal transduction regulation of SMAD protein signal transduction negative regulation of SMAD protein signal transduction mesodermal cell differentiation mesoderm morphogenesis negative regulation of cell fate specification embryo development regulation of mesodermal cell fate specification negative regulation of cell fate commitment regulation of mesodermal cell differentiation mesodermal cell fate commitment animal organ morphogenesis mesoderm formation regulation of anatomical structure morphogenesis mesoderm development mesodermal cell fate specification formation of primary germ layer regulation of animal organ morphogenesis regulation of cell fate commitment embryonic morphogenesis cell fate specification gastrulation tissue morphogenesis anatomical structure morphogenesis cell fate commitment involved in formation of primary germ layer regulation of cell fate specification negative regulation of mesodermal cell differentiation anatomical structure formation involved in morphogenesis negative regulation of mesodermal cell fate specification cell fate commitment positive regulation of JNK cascade JNK cascade positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade limb development appendage development cell morphogenesis RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process behavior system process learning learning or memory nervous system process motor learning cognition heart induction heart morphogenesis specification of animal organ identity pattern specification process developmental induction animal organ formation heart formation regionalization positive regulation of animal organ morphogenesis positive regulation of multicellular organismal process regulation of animal organ formation organ induction regulation of heart morphogenesis heart field specification mesenchyme development endocardial cushion development face morphogenesis head morphogenesis face development body morphogenesis negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of Wnt signaling pathway, calcium modulating pathway positive regulation of Wnt signaling pathway, calcium modulating pathway Wnt signaling pathway, calcium modulating pathway endoderm development endoderm formation endodermal cell differentiation neuron apoptotic process regulation of neuron apoptotic process epithelium development epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process regulation of localization import into cell 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 localization endocytosis receptor-mediated endocytosis regulation of endocytosis response to retinoic acid response to lipid response to chemical response to oxygen-containing compound endodermal cell fate specification regulation of endodermal cell differentiation regulation of endodermal cell fate specification endodermal cell fate commitment embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis cellular component disassembly cell junction organization cell junction disassembly synapse pruning synapse organization forebrain development somitogenesis chordate embryonic development segmentation anterior/posterior pattern specification embryo development ending in birth or egg hatching somite development Wnt signaling pathway involved in somitogenesis heart valve development regulation of presynapse assembly cellular component biogenesis regulation of nervous system development cellular component assembly regulation of presynapse organization negative regulation of cell junction assembly cell junction assembly regulation of synapse structure or activity negative regulation of nervous system development regulation of synapse assembly regulation of biological quality regulation of multicellular organismal development presynapse organization negative regulation of synapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization negative regulation of presynapse assembly synapse assembly negative regulation of synapse assembly presynapse assembly trans-synaptic signaling modulation of chemical synaptic transmission synaptic transmission, glutamatergic cell-cell signaling regulation of synaptic transmission, glutamatergic chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling Wnt-Frizzled-LRP5/6 complex assembly protein-containing complex organization regulation of Wnt-Frizzled-LRP5/6 complex assembly negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly negative regulation of Wnt-Frizzled-LRP5/6 complex assembly protein-containing complex assembly ossification regulation of ossification negative regulation of ossification	cell periphery cellular anatomical structure plasma membrane membrane extracellular region membrane-bounded organelle endosome membrane intracellular anatomical structure early endosome endosome intracellular vesicle early endosome membrane intracellular membrane-bounded organelle endomembrane system cell periphery cellular anatomical structure plasma membrane membrane extracellular region membrane-bounded organelle endosome membrane intracellular anatomical structure early endosome endosome intracellular vesicle early endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle cytoplasm vesicle organelle membrane
A, B	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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR039863	Dickkopf related protein 1-4	Family
C	IPR006796	Dickkopf, N-terminal cysteine-rich	Domain
C	IPR048499	Dickkopf-related protein 1/2/4, C-terminal subdomain 2	Domain
C	IPR047304	Dickkopf-related protein 1, second cysteine-rich domain	Domain
C	IPR047305	Dickkopf-related protein 1, N-terminal domain	Domain
C	IPR048500	Dickkopf-related protein 1/2/4, C-terminal subdomain 1	Domain
A, B	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A, B	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A, B	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A, B	IPR000742	EGF-like domain	Domain
A, B	IPR000033	LDLR class B repeat	Repeat
A, B	IPR050778	Cueball_EGF_LRP_Nidogen	Unknown
A, B	IPR017049	Low density lipoprotein receptor-related protein 5/6	Family
A, B	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: O94907	breast carcinoma endometriosis Malignant neoplasm of breast osteoporosis plasma cell myeloma ulcerative colitis breast cancer congestive heart failure idiopathic juvenile osteoporosis lung cancer malignant pancreatic neoplasm medulloblastoma peripheral nervous system disease psoriasis atypical teratoid rhabdoid tumor breast carcinoma endometriosis Malignant neoplasm of breast osteoporosis plasma cell myeloma ulcerative colitis breast cancer congestive heart failure idiopathic juvenile osteoporosis lung cancer malignant pancreatic neoplasm medulloblastoma peripheral nervous system disease psoriasis atypical teratoid rhabdoid tumor cutaneous lupus erythematosus interstitial cystitis malignant glioma non-small cell lung carcinoma peripheral neuropathy sinusitis bone fracture cancer cystic fibrosis esophageal adenocarcinoma glioblastoma
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.