3DVU

Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain

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	d3dvua_	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Bcl-2 inhibitors of programmed cell death	Bcl-2 inhibitors of programmed cell death	Bcl-2 homolog V-bcl-2	MuHV-4 (Murid gammaherpesvirus 4 ) [TaxId: 33708 ],	SCOPe (2.08)
B	d3dvub_	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Bcl-2 inhibitors of programmed cell death	Bcl-2 inhibitors of programmed cell death	Bcl-2 homolog V-bcl-2	MuHV-4 (Murid gammaherpesvirus 4 ) [TaxId: 33708 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8039346	3001974	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bcl-2-like inhibitors of programmed cell death	8039346	3001974	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	Bcl-2_3	e3dvuA1	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2_3	ECOD (1.6)
B	Bcl-2_3	e3dvuB1	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: Bcl-2_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (4.3.0)
B	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF15286	Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like (Bcl-2_3)	Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like	-	Family
C, D	PF15285	Beclin-1 BH3 domain, Bcl-2-interacting (BH3)	Beclin-1 BH3 domain, Bcl-2-interacting	The BH3 domain is a short motif known to bind to Bcl-xLs. This interaction is important in apoptosis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	V-bcl-2	-	regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host apoptosis biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host programmed cell death symbiont-mediated suppression of host programmed cell death regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host apoptosis biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host programmed cell death symbiont-mediated suppression of host programmed cell death regulation of killing of cells of another organism disruption of cell in another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host process regulation of cell killing symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism modulation of process of another organism killing of cells of another organism cell killing	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region
C, D	Beclin-1	phosphatidylinositol 3-kinase binding protein binding binding protein-macromolecule adaptor activity molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding identical protein binding GTPase binding kinase binding protein kinase binding	cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus intracellular signal transduction cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus intracellular signal transduction cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response cellular process activation of immune response response to chemical response to xenobiotic stimulus p38MAPK cascade intracellular signaling cassette MAPK cascade cellular response to metal ion cellular response to chemical stimulus response to metal ion response to aluminum ion cellular response to aluminum ion phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular component organization or biogenesis process utilizing autophagic mechanism regulation of catabolic process regulation of autophagy regulation of macroautophagy regulation of metabolic process cell division cellular response to nutrient levels response to nutrient levels cellular response to stress response to starvation cellular response to glucose starvation cellular response to starvation establishment of organelle localization cellular localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation establishment of localization organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization apoptotic process cell death programmed cell death response to mitochondrial depolarisation response to iron(II) ion response to iron ion negative regulation of programmed cell death negative regulation of cellular process negative regulation of biological process regulation of programmed cell death regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division regulation of cell cycle negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process JNK cascade muscle hypertrophy regulation of muscle adaptation multicellular organismal process system process positive regulation of cardiac muscle hypertrophy regulation of system process striated muscle hypertrophy regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy regulation of muscle hypertrophy muscle adaptation positive regulation of muscle hypertrophy cardiac muscle hypertrophy positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway regulation of intracellular signal transduction intrinsic apoptotic signaling pathway positive regulation of cellular process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process positive regulation of intracellular signal transduction positive regulation of apoptotic process apoptotic signaling pathway regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway positive regulation of signaling response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus cellular defense response response to nutrient response to oxygen-containing compound response to vitamin E response to vitamin positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of vacuole organization autophagosome organization cellular component biogenesis positive regulation of metabolic process cellular component assembly positive regulation of autophagosome assembly positive regulation of macroautophagy positive regulation of autophagy autophagosome assembly organelle assembly vacuole organization positive regulation of cellular component biogenesis regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of catabolic process regulation of organelle assembly positive regulation of organelle assembly cellular response to amino acid starvation response to amino acid starvation defense response to virus response to virus cellular catabolic process receptor catabolic process receptor metabolic process macromolecule metabolic process macromolecule catabolic process amyloid-beta metabolic process amide metabolic process late endosome to vacuole transport transport vacuolar transport intracellular transport vesicle-mediated transport protein-containing complex assembly negative regulation of lysosome organization negative regulation of cellular component organization lytic vacuole organization lysosome organization negative regulation of organelle organization regulation of lysosome organization cellular response to nitrogen levels cellular response to nitrogen starvation negative regulation of apoptotic process stress granule assembly membraneless organelle assembly positive regulation of stress granule assembly regulation of stress granule assembly regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction response to copper ion cellular response to copper ion cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species response to lead ion cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway SMAD protein signal transduction enzyme-linked receptor protein signaling pathway negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of organelle assembly negative regulation of autophagosome assembly negative regulation of catabolic process negative regulation of macroautophagy negative regulation of autophagy protein localization establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome cellular macromolecule localization protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein transport cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to epidermal growth factor stimulus response to epidermal growth factor response to growth factor mitophagy autophagy of mitochondrion endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport membrane organization import into cell engulfment of apoptotic cell phagocytosis, engulfment membrane invagination phagocytosis apoptotic cell clearance endocytosis plasma membrane invagination cellular response to oxygen levels cellular response to decreased oxygen levels cellular response to oxygen-glucose deprivation response to oxygen-glucose deprivation developmental process cellular developmental process cell development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development regulation of localization regulation of attachment of mitotic spindle microtubules to kinetochore attachment of mitotic spindle microtubules to kinetochore regulation of chromosome organization regulation of mitotic sister chromatid segregation regulation of chromosome segregation regulation of attachment of spindle microtubules to kinetochore positive regulation of cell cycle process positive regulation of chromosome segregation attachment of spindle microtubules to kinetochore positive regulation of attachment of spindle microtubules to kinetochore positive regulation of cell cycle regulation of sister chromatid segregation positive regulation of attachment of mitotic spindle microtubules to kinetochore regulation of metaphase plate congression	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane membrane protein complex transferase complex phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups phosphatidylinositol 3-kinase complex, class III extrinsic component of membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane membrane protein complex transferase complex phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups phosphatidylinositol 3-kinase complex, class III extrinsic component of membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane phagophore assembly site phagocytic vesicle endocytic vesicle mitochondrial membrane mitochondrion cytoplasmic side of membrane organelle outer membrane cytoplasmic side of mitochondrial outer membrane side of membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane phosphatidylinositol 3-kinase complex, class III, type I nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036834	Bcl-2-like superfamily	Homologous Superfamily
A, B	IPR029450	Apoptosis regulator M11	Family
C, D	IPR038274	Atg6/Beclin C-terminal domain superfamily	Homologous Superfamily
C, D	IPR029318	Beclin-1, BH3 domain	Domain
C, D	IPR040455	Atg6, BARA domain	Domain
C, D	IPR007243	Atg6/Beclin	Family
C, D	IPR041691	Atg6/beclin, coiled-coil domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q14457	status epilepticus myocardial infarction Lewy body dementia malignant colon neoplasm Status Epilepticus, Subclinical benign colon neoplasm lung benign neoplasm pancreatic intraductal papillary-mucinous carcinoma cancer osteosarcoma colonic neoplasm neurodegenerative disease ovarian cancer schizophrenia

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.