3V4Y

Crystal Structure of the first Nuclear PP1 holoenzyme

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3v4ya_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	Protein serine/threonine phosphatase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3v4yc1	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	Protein serine/threonine phosphatase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3v4yc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3v4ye_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	Protein serine/threonine phosphatase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3v4yg1	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	Protein serine/threonine phosphatase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3v4yg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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)
C	SCOP2B Superfamily	Metallo-dependent phosphatases	8080445	3001067	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-dependent phosphatases	8080445	3001067	SCOP2B (2022-06-29)
G	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)
A	PF00149,PF16891	e3v4yA1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PF00149,PF16891	ECOD (1.6)
C	PF00149,PF16891	e3v4yC2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PF00149,PF16891	ECOD (1.6)
E	PF00149,PF16891	e3v4yE2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PF00149,PF16891	ECOD (1.6)
G	PF00149,PF16891	e3v4yG2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PF00149,PF16891	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
C	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
E	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
G	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
B	6.10.250.1290	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
H	6.10.250.1290	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	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, C, E, G	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
A, C, E, G	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 ribonucleoprotein complex binding protein-containing complex binding myosin phosphatase activity protein phosphatase binding phosphatase binding protein phosphatase 1 binding enzyme binding cation binding ion binding metal ion binding small molecule 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 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 regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds cellular biosynthetic process regulation of glucan biosynthetic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process regulation of primary metabolic process polysaccharide metabolic process organic substance metabolic process glucan metabolic process organic substance biosynthetic process regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process cellular metabolic process glycogen metabolic process primary metabolic process regulation of cellular metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of polysaccharide biosynthetic process metabolic process energy reserve metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of carbohydrate biosynthetic process regulation of glycogen metabolic process regulation of metabolic process rhythmic process circadian rhythm regulation of circadian rhythm 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 organonitrogen compound metabolic process dephosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus 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 organic substance catabolic process circadian regulation of gene expression gene expression regulation of gene expression cell cycle response to light stimulus entrainment of circadian clock response to external stimulus photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod response to metal ion response to chemical response to lead ion response to inorganic substance organonitrogen compound biosynthetic process post-transcriptional regulation of gene expression translational initiation regulation of translational initiation regulation of protein metabolic process translation regulation of translation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle somatodendritic compartment cell body perikaryon neuronal cell body phosphatase complex protein-containing complex protein phosphatase type 1 complex catalytic complex cytoplasm protein serine/threonine phosphatase complex PTW/PP1 phosphatase complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane presynapse synapse cell junction nucleoplasm glutamatergic synapse cell-cell junction adherens junction anchoring junction glycogen granule neuron spine neuron projection dendritic spine plasma membrane bounded cell projection cell projection postsynapse dendrite dendritic tree
B, D, F, H	Nuclear inhibitor of protein phosphatase 1	DNA binding binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding ribonuclease E activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity DNA binding binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding ribonuclease E activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity 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 protein serine/threonine phosphatase inhibitor activity endonuclease activity	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process RNA catabolic process RNA splicing cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process biosynthetic process organic substance biosynthetic process cellular process RNA processing cell population proliferation negative regulation of protein dephosphorylation protein dephosphorylation regulation of cellular process regulation of protein modification process negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of cellular process negative regulation of protein modification process negative regulation of dephosphorylation protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process organonitrogen compound metabolic process regulation of dephosphorylation regulation of protein dephosphorylation dephosphorylation negative regulation of metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorus metabolic process regulation of metabolic process mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, C, E, G	IPR031675	Serine-threonine protein phosphatase, N-terminal	Domain
A, C, E, G	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, C, E, G	IPR006186	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase	Domain
B, D, F, H	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
B, D, F, H	IPR000253	Forkhead-associated (FHA) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: P62136	lung adenocarcinoma osteosarcoma severe acute respiratory syndrome lymphoplasmacytic lymphoma ovarian cancer Middle East respiratory syndrome plasma cell myeloma
B, D, F, H	Pharos: Q12972	lung cancer 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 R01GM133198.