3EGH | pdb_00003egh

Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8080445	3001067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8080445	3001067	SCOP2B (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	EXOSC1	e3eghC1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: EXOSC1	ECOD (v294.1)
D	N6_Mtase	e3eghD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
A	RVP	e3eghA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
B	RVP	e3eghB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
B	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF17817	PDZ domain (PDZ_5)	PDZ domain	This entry corresponds to PDZ domains found in neurabin and spinophilin proteins [1]. The PDZ domain in spinophilin mediates its interaction with protein phosphatase PP1 [1].	Domain
C, D	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
A, B	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain
A, B	PF16891	Serine-threonine protein phosphatase N-terminal domain (STPPase_N)	Serine-threonine protein phosphatase N-terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	nodularin R	-	-	-
C, D	Spinophilin	enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity binding nucleic acid binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity binding nucleic acid binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding actin filament binding protein phosphatase binding phosphatase binding protein phosphatase 1 binding enzyme binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups D2 dopamine receptor binding signaling receptor binding G protein-coupled receptor binding dopamine receptor binding kinase binding transmembrane transporter binding	response to stimulus response to chemical response to xenobiotic stimulus behavior multicellular organismal process system process learning learning or memory nervous system process cognition developmental process multicellular organism development reproductive system development anatomical structure development response to stimulus response to chemical response to xenobiotic stimulus behavior multicellular organismal process system process learning learning or memory nervous system process cognition developmental process multicellular organism development reproductive system development anatomical structure development system development positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of protein localization to plasma membrane cellular response to nitrogen compound cellular response to stimulus response to morphine response to isoquinoline alkaloid response to nitrogen compound cellular response to isoquinoline alkaloid cellular response to morphine response to alkaloid cellular response to chemical stimulus cellular response to alkaloid cellular component disassembly actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization cellular component organization organelle organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of growth regulation of cellular component organization negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth negative regulation of growth negative regulation of cellular process cell migration cell motility reproductive process male mating behavior multicellular organismal reproductive process reproductive behavior mating behavior response to peptide cellular response to peptide head development forebrain development animal organ development brain development nervous system development pallium development cerebral cortex development central nervous system development telencephalon development response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to acid chemical response to kainic acid response to oxygen-containing compound response to amino acid response to L-phenylalanine derivative cellular response to xenobiotic stimulus plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development generation of neurons neurogenesis neuron differentiation cell differentiation neuron development hippocampus development limbic system development regulation of opioid receptor signaling pathway regulation of signaling signaling regulation of signal transduction cell communication G protein-coupled opioid receptor signaling pathway regulation of response to stimulus regulation of cell communication G protein-coupled receptor signaling pathway signal transduction regulation of G protein-coupled receptor signaling pathway intracellular signal transduction calcium-mediated signaling intracellular signaling cassette dendrite development cellular component biogenesis cellular component assembly regulation of postsynapse assembly cell junction assembly regulation of synapse structure or activity synapse organization regulation of synapse assembly regulation of biological quality postsynapse organization postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly response to ketone response to prostaglandin response to alcohol response to prostaglandin E filopodium assembly plasma membrane bounded cell projection assembly cell projection assembly response to immobilization stress response to stress cellular response to oxygen-containing compound cellular response to lipid response to estradiol cellular response to estradiol stimulus response to amine response to amphetamine regulation of protein localization to actin cortical patch protein localization to actin cytoskeleton positive regulation of protein localization to cell cortex positive regulation of protein localization to actin cortical patch protein localization to actin cortical patch regulation of protein localization to cell cortex protein localization to cytoskeleton protein localization to organelle protein localization to cell cortex developmental process involved in reproduction cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to epidermal growth factor stimulus response to epidermal growth factor response to growth factor response to nicotine	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton extrinsic component of plasma membrane synapse cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton extrinsic component of plasma membrane synapse membrane plasma membrane synaptic membrane cell periphery extrinsic component of synaptic membrane postsynapse postsynaptic membrane cell junction plasma membrane region extrinsic component of membrane extrinsic component of postsynaptic membrane somatodendritic compartment dendrite dendritic tree neuron projection cytoplasm glutamatergic synapse cell-cell junction adherens junction anchoring junction neuron spine dendritic spine neuron projection membrane dendrite membrane leading edge membrane dendritic spine membrane cell projection membrane cell body neuronal cell body dendritic spine neck actin-based cell projection filopodium ruffle ruffle membrane dendritic spine head growth cone axon distal axon site of polarized growth membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cell cortex cortical cytoskeleton cortical actin cytoskeleton cytoplasmic side of membrane cytoplasmic side of dendritic spine plasma membrane cytoplasmic side of plasma membrane side of membrane postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse endomembrane system spine apparatus
A, B	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	phosphoric ester hydrolase activity phosphoprotein phosphatase activity protein serine/threonine phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity cell adhesion molecule binding cadherin binding involved in cell-cell adhesion cadherin binding protein binding binding cell adhesion mediator activity phosphoric ester hydrolase activity phosphoprotein phosphatase activity protein serine/threonine phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity cell adhesion molecule binding cadherin binding involved in cell-cell adhesion cadherin binding protein binding binding cell adhesion mediator activity cell-cell adhesion mediator activity protein phosphatase binding phosphatase binding protein phosphatase 1 binding enzyme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat phosphatase activity RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ribonucleoprotein complex binding protein-containing complex binding	cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication cellular process signal transduction Wnt signaling pathway telomere maintenance in response to DNA damage telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization cellular response to stress DNA damage response response to stress metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of protein stability regulation of biological quality protein stabilization developmental process multicellular organismal process epithelium development tube development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis morphogenesis of a branching structure anatomical structure development epithelial tube morphogenesis morphogenesis of a branching epithelium cell division positive regulation of cell communication positive regulation of signal transduction signal transduction in absence of ligand positive regulation of biological process regulation of programmed cell death positive regulation of extrinsic apoptotic signaling pathway in absence of ligand extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus extrinsic apoptotic signaling pathway in absence of ligand positive regulation of cellular process positive regulation of programmed cell death regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway cell death positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway in absence of ligand apoptotic process programmed cell death regulation of apoptotic signaling pathway positive regulation of signaling protein dephosphorylation dephosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translation in response to stress translational initiation regulation of biosynthetic process regulation of translational initiation regulation of protein metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of translational initiation in response to stress regulation of macromolecule biosynthetic process regulation of metabolic process transcription elongation by RNA polymerase II negative regulation of biological process RNA metabolic process negative regulation of transcription elongation by RNA polymerase II negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process 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 DNA-templated transcription elongation negative regulation of DNA-templated transcription regulation of transcription elongation by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process negative regulation of DNA-templated transcription, elongation DNA-templated transcription elongation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process rhythmic process circadian regulation of gene expression circadian rhythm response to light stimulus entrainment of circadian clock response to external stimulus regulation of circadian rhythm photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod promoter clearance during DNA-templated transcription RNA polymerase II promoter clearance regulation of generation of precursor metabolites and energy positive regulation of macromolecule biosynthetic process positive regulation of glycogen metabolic process positive regulation of metabolic process regulation of small molecule metabolic process small molecule metabolic process positive regulation of macromolecule metabolic process carbohydrate biosynthetic process hexose metabolic process positive regulation of glucose metabolic process positive regulation of glycogen biosynthetic process energy reserve metabolic process positive regulation of carbohydrate metabolic process regulation of glycogen metabolic process monosaccharide metabolic process regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process regulation of polysaccharide metabolic process polysaccharide metabolic process glucan metabolic process positive regulation of biosynthetic process regulation of carbohydrate metabolic process regulation of glucose metabolic process carbohydrate metabolic process polysaccharide biosynthetic process glycogen metabolic process generation of precursor metabolites and energy glycogen biosynthetic process regulation of polysaccharide biosynthetic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process animal organ development respiratory tube development lung development respiratory system development system development catabolic process carbohydrate catabolic process macromolecule catabolic process regulation of glycogen catabolic process glycogen catabolic process regulation of carbohydrate catabolic process glucan catabolic process regulation of catabolic process polysaccharide catabolic process protein-containing complex disassembly regulation of protein-containing complex disassembly regulation of termination of RNA polymerase II transcription, poly(A)-coupled cellular component disassembly termination of RNA polymerase II transcription, poly(A)-coupled positive regulation of RNA metabolic process regulation of termination of DNA-templated transcription termination of RNA polymerase II transcription regulation of termination of RNA polymerase II transcription regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA-templated transcription DNA-templated transcription termination positive regulation of termination of DNA-templated transcription positive regulation of termination of RNA polymerase II transcription positive regulation of protein-containing complex disassembly protein-containing complex organization positive regulation of RNA biosynthetic process positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled response to metal ion response to chemical response to lead ion positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body phosphatase complex protein-containing complex protein phosphatase type 1 complex intracellular anatomical structure catalytic complex cytoplasm protein serine/threonine phosphatase complex PTW/PP1 phosphatase complex extracellular exosome somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body phosphatase complex protein-containing complex protein phosphatase type 1 complex intracellular anatomical structure catalytic complex cytoplasm protein serine/threonine phosphatase complex PTW/PP1 phosphatase complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cytosol cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection synapse cell junction glutamatergic synapse cell-cell junction adherens junction anchoring junction glycogen granule neuron spine neuron projection dendritic spine postsynapse dendrite dendritic tree nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen membraneless organelle nuclear lumen sperm end piece microtubule organizing center cytoskeleton centriole microtubule cytoskeleton cell periphery plasma membrane membrane presynapse nucleoplasm endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR036034	PDZ superfamily	Homologous Superfamily
C, D	IPR043446	Neurabin-like family	Family
C, D	IPR001478	PDZ domain	Domain
C, D	IPR040645	Neurabin-1/2, PDZ domain	Domain
A, B	IPR050341	Serine/threonine-protein phosphatase PP1 catalytic subunit	Family
A, B	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, B	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
A, B	IPR031675	Serine-threonine protein phosphatase, N-terminal	Domain
A, B	IPR006186	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P62136	lung adenocarcinoma osteosarcoma severe acute respiratory syndrome lymphoplasmacytic lymphoma ovarian cancer Middle East respiratory syndrome plasma cell myeloma

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.