5B4X | pdb_00005b4x

Crystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment

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)
D	SGL_5	e5b4xD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: SGL_5	ECOD (1.6)
D	FXa_inhibition	e5b4xD3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: FXa_inhibition	ECOD (1.6)
D	EGF_CA	e5b4xD2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_CA	ECOD (1.6)
D	Ldl_recept_a	e5b4xD6	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)
B	SGL_5	e5b4xB2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: SGL_5	ECOD (1.6)
B	FXa_inhibition	e5b4xB5	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: FXa_inhibition	ECOD (1.6)
B	EGF_CA	e5b4xB4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_CA	ECOD (1.6)
B	Ldl_recept_a	e5b4xB6	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)
C	Reelin_subrepeat_2	e5b4xC2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Reelin_subrepeat_2	ECOD (1.6)
C	EGF_2	e5b4xC1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_2	ECOD (1.6)
C	EGF_2_like	e5b4xC4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_2_like	ECOD (1.6)
A	Reelin_subrepeat_2	e5b4xA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Reelin_subrepeat_2	ECOD (1.6)
A	EGF_2	e5b4xA5	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_2	ECOD (1.6)
A	EGF_2_like	e5b4xA6	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_2_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	PF07645	Calcium-binding EGF domain (EGF_CA)	Calcium-binding EGF domain		Domain
B, D	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
B, D	PF00058	Low-density lipoprotein receptor repeat class B (Ldl_recept_b)	Low-density lipoprotein receptor repeat class B	-	Repeat
A, C	PF21471	Reelin subrepeat B (Reelin_subrepeat-B)	Reelin subrepeat B	Reelin is an extracellular matrix serine protease that plays a role in layering of neurons in the cerebral cortex and cerebellum. It regulates microtubule function in neurons and neuronal migration. It binds to the extracellular domains of lipoprotei ...	Reelin is an extracellular matrix serine protease that plays a role in layering of neurons in the cerebral cortex and cerebellum. It regulates microtubule function in neurons and neuronal migration. It binds to the extracellular domains of lipoprotein receptors VLDLR and LRP8/APOER2 which induces tyrosine phosphorylation of DAB1 and modulation of TAU phosphorylation. Reelin consists of a signal sequence, an F-spondin-like region and nine sequentially concatenated repeat units. Each complete reelin repeat contains a central epidermal growth factor (EGF) module flanked by two subrepeats of 150-190 amino acids (subrepeats A and B) [1-3]. This entry represents subrepeat B (also referred to R3B) which adopts a beta jelly-roll fold similar to bacterial xylanase. They contain the signature Asp-box motif [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e	reelin receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity amide binding amyloid-beta binding binding peptide binding lipoprotein particle binding protein-containing complex binding protein-lipid complex binding high-density lipoprotein particle binding cation binding ion binding reelin receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity amide binding amyloid-beta binding binding peptide binding lipoprotein particle binding protein-containing complex binding protein-lipid complex binding high-density lipoprotein particle binding cation binding ion binding calcium ion binding metal ion binding small molecule binding apolipoprotein binding protein binding cytoskeletal protein binding kinesin binding lipoprotein particle receptor activity cargo receptor activity very-low-density lipoprotein particle receptor activity low-density lipoprotein particle receptor activity calcium-dependent protein binding	response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus response to sterol 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 cellular response to lipid cellular process response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus response to sterol 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 cellular response to lipid cellular process cellular response to sterol cellular response to cholesterol multicellular organismal process cellular developmental process forebrain development glial cell migration telencephalon glial cell migration cerebral cortex development multicellular organism development neurogenesis telencephalon cell migration forebrain cell migration gliogenesis cell differentiation anatomical structure development cell migration cell motility system development layer formation in cerebral cortex developmental process cerebral cortex cell migration head development animal organ development brain development nervous system development cerebral cortex radially oriented cell migration pallium development anatomical structure morphogenesis central nervous system development anatomical structure formation involved in morphogenesis cerebral cortex radial glia-guided migration telencephalon development regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide cellular response to cytokine stimulus signal transduction ammon gyrus development hippocampus development limbic system development regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication reelin-mediated signaling pathway diterpenoid metabolic process retinoid metabolic process primary metabolic process metabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process positive regulation of dendritic spine morphogenesis positive regulation of nervous system development cell projection organization positive regulation of dendritic spine development regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell morphogenesis regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of dendrite morphogenesis regulation of synapse structure or activity positive regulation of cell projection organization synapse organization regulation of biological quality dendritic spine morphogenesis dendritic spine development postsynapse organization dendritic spine organization regulation of cell projection organization positive regulation of cell development regulation of postsynapse organization positive regulation of cell morphogenesis generation of neurons regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development regulation of dendritic spine development cell morphogenesis cellular component organization regulation of nervous system development dendrite development positive regulation of neuron projection development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization dendrite morphogenesis positive regulation of dendrite morphogenesis cell morphogenesis involved in neuron differentiation regulation of synapse organization cell junction organization neuron development regulation of dendritic spine morphogenesis neuron projection organization regulation of plasma membrane bounded cell projection organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus immune response response to other organism defense response regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism regulation of immune response spinal cord development ventral spinal cord development cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor positive regulation of dendrite development proteolysis protein metabolic process macromolecule metabolic process	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection glutamatergic synapse protein-containing complex receptor complex cell body neuronal cell body axon intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle microtubule associated complex intracellular membraneless organelle microtubule cytoskeleton extracellular region extracellular space cell surface membrane microdomain membrane raft plasma membrane raft caveola Schaffer collateral - CA1 synapse
A, C	Reelin	cation binding ion binding binding metal ion binding small molecule binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity peptidase activity serine hydrolase activity cation binding ion binding binding metal ion binding small molecule binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular developmental process forebrain development glial cell migration telencephalon glial cell migration developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular developmental process forebrain development glial cell migration telencephalon glial cell migration cerebral cortex development neurogenesis telencephalon cell migration forebrain cell migration gliogenesis cell differentiation cell migration cell motility layer formation in cerebral cortex cerebral cortex cell migration cerebral cortex radially oriented cell migration pallium development anatomical structure morphogenesis anatomical structure formation involved in morphogenesis cellular process cerebral cortex radial glia-guided migration telencephalon development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling behavior learning learning or memory cognition regulation of localization transport regulation of signaling receptor activity monoatomic ion transmembrane transport regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport localization positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport regulation of transport regulation of monoatomic ion transport establishment of localization transmembrane transport regulation of molecular function positive regulation of AMPA receptor activity regulation of transmembrane transport positive regulation of transport positive regulation of transporter activity regulation of neurotransmitter receptor activity positive regulation of ion transmembrane transporter activity regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process cellular component organization positive regulation of developmental process regulation of synapse structure or activity synapse organization cellular component organization or biogenesis developmental maturation synapse maturation regulation of synapse organization regulation of synapse maturation cell junction organization positive regulation of synapse maturation intracellular signal transduction regulation of intracellular signal transduction positive regulation of TOR signaling TOR signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process lateral motor column neuron migration neuron migration spinal cord motor neuron migration motor neuron migration generation of neurons positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process positive regulation of kinase activity regulation of protein tyrosine kinase activity regulation of kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation protein metabolic process positive regulation of protein kinase activity positive regulation of protein tyrosine kinase activity regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation peptidyl-tyrosine phosphorylation membrane organization cellular localization postsynapse organization localization within membrane protein localization to membrane organelle organization postsynaptic density protein 95 clustering postsynaptic density organization macromolecule localization postsynaptic specialization organization intracellular protein localization postsynaptic membrane organization regulation of behavior regulation of neuron projection development cell projection organization cell development neuron projection development neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization neuron development regulation of plasma membrane bounded cell projection organization cell morphogenesis reelin-mediated signaling pathway cell adhesion neurotransmitter-gated ion channel clustering receptor clustering NMDA glutamate receptor clustering cerebral cortex tangential migration glial cell differentiation positive regulation of DNA-binding transcription factor activity positive regulation of CREB transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription positive regulation of dendritic spine morphogenesis positive regulation of nervous system development positive regulation of dendritic spine development regulation of cell differentiation regulation of neurogenesis regulation of cell morphogenesis regulation of cell development cell projection morphogenesis neuron projection morphogenesis regulation of dendrite morphogenesis dendritic spine morphogenesis dendritic spine development dendritic spine organization positive regulation of cell development regulation of postsynapse organization positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process plasma membrane bounded cell projection morphogenesis regulation of dendritic spine development regulation of nervous system development dendrite development positive regulation of cell differentiation positive regulation of neurogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development dendrite morphogenesis positive regulation of dendrite morphogenesis cell morphogenesis involved in neuron differentiation regulation of dendritic spine morphogenesis neuron projection organization response to stress multicellular organismal response to stress response to pain locomotory behavior hippocampus development limbic system development regulation of synaptic activity long-term synaptic potentiation positive regulation of long-term synaptic potentiation regulation of synaptic plasticity positive regulation of synaptic transmission regulation of long-term synaptic potentiation synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic pattern specification process regionalization spinal cord development spinal cord patterning regulation of NMDA receptor activity protein localization to synapse protein localization to cell junction receptor localization to synapse cellular component biogenesis cellular component assembly cell junction assembly organelle assembly postsynaptic specialization assembly postsynapse assembly excitatory synapse assembly synapse assembly postsynaptic density assembly regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signaling cassette positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cell motility regulation of neuron migration regulation of locomotion regulation of cell migration locomotion long-term memory memory positive regulation of locomotion positive regulation of motor neuron migration positive regulation of cell migration positive regulation of cell motility regulation of lateral motor column neuron migration positive regulation of lateral motor column neuron migration regulation of motor neuron migration positive regulation of neuron migration ventral spinal cord development regulation of neuron differentiation axonogenesis axon guidance axon development neuron projection guidance interneuron migration associative learning small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction positive regulation of small GTPase mediated signal transduction proteolysis	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm protein-containing complex reelin complex extracellular region extracellular space cell periphery somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm protein-containing complex reelin complex extracellular region extracellular space cell periphery plasma membrane membrane extracellular matrix external encapsulating structure

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B, D	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
B, D	IPR049883	NOTCH1 EGF-like calcium-binding domain	Domain
B, D	IPR000033	LDLR class B repeat	Repeat
B, D	IPR001881	EGF-like calcium-binding domain	Domain
B, D	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
B, D	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
B, D	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
B, D	IPR000742	EGF-like domain	Domain
B, D	IPR051221	Low-density lipoprotein receptor-related	Family
B, D	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A, C	IPR049419	Reelin, subrepeat B	Repeat
A, C	IPR036278	Sialidase superfamily	Homologous Superfamily
A, C	IPR034968	Reelin	Family
A, C	IPR000742	EGF-like domain	Domain
A, C	IPR042307	Reeler domain superfamily	Homologous Superfamily
A, C	IPR002861	Reeler domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q14114	myocardial infarction Nerve Degeneration ovarian cancer Pick disease schizophrenia tuberculosis breast cancer glioblastoma lung cancer malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer Sjogren syndrome ulcerative colitis myocardial infarction Nerve Degeneration ovarian cancer Pick disease schizophrenia tuberculosis breast cancer glioblastoma lung cancer malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer Sjogren syndrome ulcerative colitis atopic eczema Crohn disease invasive ductal breast carcinoma major depressive disorder malignant glioma myocardial infarction, susceptibility to osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor cutaneous lupus erythematosus lung adenocarcinoma malignant colon neoplasm medulloblastoma

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.