3V64 | pdb_00003v64

Crystal Structure of agrin and LRP4

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth B]	d3v64b_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth A]	d3v64a1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth A]	d3v64a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8079972	3000120	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	Laminin G-like module	8079971	4002689	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Concanavalin A-like lectins/glucanases	8079972	3000120	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth B]	SmpA_OmlA	e3v64B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)
B [auth A]	PUF	e3v64A1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PUF	ECOD (develop294)
D	FXa_inhibition	e3v64D4	A: alpha bundles	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 (develop294)
D	Sigma70_r2,Sigma70_ner	e3v64D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
A [auth C]	Ephrin_lbd	e3v64C4	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ephrin_lbd	ECOD (develop294)
A [auth C]	Sigma70_r2,Sigma70_ner	e3v64C2	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B [auth A]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
D	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)
A [auth C]	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
A [auth C]	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
B [auth A], C [auth B]	PF00054	Laminin G domain (Laminin_G_1)	Laminin G domain		Domain
A [auth C], D	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 A], C [auth B]	Isoform 4 of Agrin	glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding neurotransmitter receptor regulator activity acetylcholine receptor regulator activity molecular function regulator activity signaling receptor regulator activity molecular function inhibitor activity ATPase inhibitor activity ATPase regulator activity BMP binding protein binding glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding neurotransmitter receptor regulator activity acetylcholine receptor regulator activity molecular function regulator activity signaling receptor regulator activity molecular function inhibitor activity ATPase inhibitor activity ATPase regulator activity BMP binding protein binding cytokine binding transporter inhibitor activity transporter regulator activity heparan sulfate proteoglycan binding proteoglycan binding sialic acid binding organic acid binding ion binding anion binding carboxylic acid binding small molecule binding cation binding calcium ion binding metal ion binding dystroglycan binding molecular function activator activity receptor ligand activity signaling receptor activator activity transforming growth factor beta binding growth factor binding transmembrane transporter binding	protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle cellular process protein localization to postsynapse intracellular protein localization regulation of biological quality protein localization to cell junction receptor localization to synapse regulation of localization regulation of cellular process regulation of protein localization positive regulation of biological process cellular component organization neuromuscular junction development receptor clustering synapse organization cellular component organization or biogenesis regulation of skeletal muscle acetylcholine-gated channel clustering regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane positive regulation of cellular process membrane organization regulation of biological process postsynapse organization positive regulation of receptor clustering skeletal muscle acetylcholine-gated channel clustering positive regulation of protein localization to membrane positive regulation of skeletal muscle acetylcholine-gated channel clustering cell junction organization regulation of cellular localization positive regulation of protein localization plasma membrane organization endomembrane system organization transport sodium ion export across plasma membrane monoatomic ion transmembrane transport negative regulation of monoatomic ion transport negative regulation of biological process sodium ion transmembrane transport negative regulation of transport regulation of monoatomic ion transmembrane transport export across plasma membrane regulation of sodium ion transport metal ion transport regulation of sodium ion transmembrane transport negative regulation of transmembrane transport monoatomic cation transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport negative regulation of cation transmembrane transport negative regulation of sodium ion export across plasma membrane monoatomic cation transport regulation of metal ion transport regulation of transport regulation of monoatomic ion transport regulation of sodium ion export across plasma membrane export from cell negative regulation of sodium ion transmembrane transport establishment of localization transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport negative regulation of sodium ion transport sodium ion transport trans-synaptic signaling synaptic signaling signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission cell communication developmental process multicellular organismal process nervous system development cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development synapse assembly system development 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 transcription by RNA polymerase II 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 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 cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling Rac protein signal transduction positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling cellular developmental process cell differentiation rhythmic process circadian rhythm modulation of chemical synaptic transmission regulation of synaptic activity regulation of trans-synaptic signaling regulation of synapse structure or activity neuron apoptotic process positive regulation of programmed cell death positive regulation of motor neuron apoptotic process regulation of apoptotic process regulation of programmed cell death motor neuron apoptotic process cell death regulation of motor neuron apoptotic process positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of neuron apoptotic process regulation of neuron apoptotic process axonogenesis cell projection organization neuron projection development cell projection morphogenesis neuron differentiation neuron projection morphogenesis taxis regulation of axon guidance chemotaxis regulation of cell projection organization response to external stimulus generation of neurons response to chemical regulation of locomotion regulation of neuron projection development regulation of cellular component organization regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis neurogenesis locomotion plasma membrane bounded cell projection organization axon guidance axon development regulation of chemotaxis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection guidance neuron development regulation of plasma membrane bounded cell projection organization establishment of protein localization protein transport regulation of synapse organization heart process system process regulation of heart contraction regulation of system process regulation of cardiac muscle contraction cardiac muscle contraction muscle contraction muscle system process regulation of muscle system process striated muscle contraction circulatory system process regulation of blood circulation regulation of striated muscle contraction regulation of muscle contraction regulation of multicellular organismal process heart contraction blood circulation regulation of cytoskeleton organization microtubule cytoskeleton organization regulation of microtubule-based process regulation of organelle organization organelle organization microtubule-based process regulation of microtubule cytoskeleton organization cytoskeleton organization regulation of cardiac muscle cell membrane potential regulation of membrane potential filopodium assembly plasma membrane bounded cell projection assembly cell projection assembly cell surface receptor signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of neuromuscular junction development positive regulation of nervous system development regulation of growth developmental growth positive regulation of developmental process regulation of synaptic assembly at neuromuscular junction regulation of neuromuscular junction development positive regulation of developmental growth positive regulation of synaptic assembly at neuromuscular junction regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly positive regulation of cellular component organization regulation of developmental process regulation of nervous system development regulation of synapse assembly regulation of multicellular organismal development regulation of developmental growth positive regulation of cellular component biogenesis growth regulation of cellular component biogenesis positive regulation of cell junction assembly positive regulation of growth synaptic assembly at neuromuscular junction	basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure sarcolemma plasma membrane membrane synapse cell junction glutamatergic synapse extracellular region extracellular space growth cone basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure sarcolemma plasma membrane membrane synapse cell junction glutamatergic synapse extracellular region extracellular space growth cone axon cell projection distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth cell surface
A [auth C], D	Low-density lipoprotein receptor-related protein 4	molecular transducer activity coreceptor activity signaling receptor activity protein tyrosine kinase binding protein binding binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding cation binding ion binding calcium ion binding molecular transducer activity coreceptor activity signaling receptor activity protein tyrosine kinase binding protein binding binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding cation binding ion binding calcium ion binding metal ion binding small molecule binding apolipoprotein binding scaffold protein binding identical protein binding protein homodimerization activity protein dimerization activity	regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process cellular component organization localization neuromuscular junction development receptor clustering synapse organization cellular component organization or biogenesis intracellular protein localization regulation of skeletal muscle acetylcholine-gated channel clustering regulation of receptor clustering regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process cellular component organization localization neuromuscular junction development receptor clustering synapse organization cellular component organization or biogenesis intracellular protein localization regulation of skeletal muscle acetylcholine-gated channel clustering regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane positive regulation of cellular process membrane organization regulation of biological process postsynapse organization positive regulation of receptor clustering skeletal muscle acetylcholine-gated channel clustering biological regulation positive regulation of protein localization to membrane localization within membrane protein localization to membrane positive regulation of skeletal muscle acetylcholine-gated channel clustering cell junction organization regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process multicellular organismal process catabolic process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic process metabolic process amyloid-beta clearance developmental process dorsal/ventral pattern formation multicellular organism development anatomical structure development pattern specification process regionalization cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway 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 small GTPase-mediated signal transduction Rac protein signal transduction intracellular signal transduction intracellular signaling cassette limb development appendage development cellular developmental process nervous system development generation of neurons neurogenesis cell differentiation system development axonogenesis cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation neuron projection morphogenesis negative regulation of cellular component organization regulation of cell projection organization negative regulation of axonogenesis negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis regulation of nervous system development negative regulation of neurogenesis regulation of axonogenesis negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization negative regulation of developmental process axon development negative regulation of neuron projection development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis negative regulation of cell development neuron development regulation of plasma membrane bounded cell projection organization animal organ development kidney development renal system development positive regulation of cell communication positive regulation of signal transduction regulation of small GTPase mediated signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of signaling odontogenesis of dentin-containing tooth odontogenesis animal organ morphogenesis presynapse organization membrane biogenesis presynaptic membrane assembly membrane assembly cellular component biogenesis presynaptic membrane organization cellular component assembly cell junction assembly synapse assembly presynapse assembly import into cell transport endocytosis establishment of localization vesicle-mediated transport epithelium development epidermis development molting cycle process hair cycle tissue development skin development skin epidermis development hair follicle development molting cycle hair cycle process dendrite development dendrite morphogenesis developmental growth growth synaptic assembly at neuromuscular junction positive regulation of presynaptic membrane organization positive regulation of cellular component organization regulation of presynaptic membrane organization regulation of synapse organization regulation of synapse structure or activity regulation of biological quality embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development appendage morphogenesis limb morphogenesis regulation of postsynapse assembly regulation of synapse assembly postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of cell junction assembly enzyme-linked receptor protein signaling pathway postsynaptic membrane assembly ossification regulation of ossification negative regulation of ossification proximal/distal pattern formation embryonic digit morphogenesis	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection neuromuscular junction synapse cell junction cell body neuronal cell body cell periphery membrane somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection neuromuscular junction synapse cell junction cell body neuronal cell body cell periphery membrane plasma membrane plasma membrane region synaptic membrane cell surface postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization organelle asymmetric synapse membrane microdomain membrane raft plasma membrane raft

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], C [auth B]	IPR050372	Neurexin-related cell adhesion and synaptic protein	Family
B [auth A], C [auth B]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B [auth A], C [auth B]	IPR002049	Laminin-type EGF domain	Domain
B [auth A], C [auth B]	IPR003884	Factor I / membrane attack complex	Domain
B [auth A], C [auth B]	IPR003645	Follistatin-like, N-terminal	Domain
B [auth A], C [auth B]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth A], C [auth B]	IPR036364	SEA domain superfamily	Homologous Superfamily
B [auth A], C [auth B]	IPR000082	SEA domain	Domain
B [auth A], C [auth B]	IPR036058	Kazal domain superfamily	Homologous Superfamily
B [auth A], C [auth B]	IPR002350	Kazal domain	Domain
B [auth A], C [auth B]	IPR000742	EGF-like domain	Domain
B [auth A], C [auth B]	IPR001791	Laminin G domain	Domain
A [auth C], D	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A [auth C], D	IPR026823	Complement Clr-like EGF domain	Domain
A [auth C], D	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A [auth C], D	IPR000033	LDLR class B repeat	Repeat
A [auth C], D	IPR001881	EGF-like calcium-binding domain	Domain
A [auth C], D	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
A [auth C], D	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A [auth C], D	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A [auth C], D	IPR000742	EGF-like domain	Domain
A [auth C], D	IPR051221	Low-density lipoprotein receptor-related	Family
A [auth C], D	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily