5DFZ | pdb_00005dfz

Structure of Vps34 complex II from S. cerevisiae.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth D]	SCOP2B Superfamily	BARA domain-like	8090325	3002431	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)
E [auth D]	APG6	e5dfzD1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (develop294)
E [auth D]	Aldedh	e5dfzD2	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Aldedh	ECOD (develop294)
D [auth E]	Peripla_BP_4	e5dfzE1	A: alpha bundles	X: Hsp90 co-chaperone CDC37 middle domain	H: Lysozyme-like	T: Lysozyme-like	F: Peripla_BP_4	ECOD (develop294)
C [auth B]	Pkinase	e5dfzB1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Pkinase	ECOD (develop294)
C [auth B]	GP120	e5dfzB2	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: GP120	ECOD (develop294)
B [auth C]	Peripla_BP_4	e5dfzC1	A: alpha bundles	X: Hsp90 co-chaperone CDC37 middle domain	H: Lysozyme-like	T: Lysozyme-like	F: Peripla_BP_4	ECOD (develop294)
A	VPS38	e5dfzA1	A: alpha bundles	X: PH domain-like	H: PH domain-like	T: PH domain-like	F: VPS38	ECOD (develop294)
A	UDPG_MGDP_dh	e5dfzA2	A: alpha bundles	X: PH domain-like	H: PH domain-like	T: PH domain-like	F: UDPG_MGDP_dh	ECOD (develop294)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth E]	Heavy Chain	IGHV1	-	phosphatidylinositol 3-kinase vps34	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth D]	PF04111	Apg6 BARA domain (APG6)	Apg6 BARA domain	In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the ...	In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [2]. This entry is the Beta-Alpha repeated, autophagy-specific (BARA) domain [3].	Domain
C [auth B]	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
B [auth C]	PF00613	Phosphoinositide 3-kinase family, accessory domain (PIK domain) (PI3Ka)	Phosphoinositide 3-kinase family, accessory domain (PIK domain)	-	Repeat
B [auth C]	PF00792	Phosphoinositide 3-kinase C2 (PI3K_C2)	Phosphoinositide 3-kinase C2	Phosphoinositide 3-kinase region postulated to contain a C2 domain. Outlier of Pfam:PF00168 family.	Domain
B [auth C]	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth G]	Putative N-terminal domain of S. cerevisiae Vps30	-	-	-
E [auth D]	Vacuolar protein sorting-associated protein 30	phosphatidylinositol 3-kinase binding protein binding binding protein-macromolecule adaptor activity molecular adaptor activity	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism phosphatidylinositol metabolic process glycerophospholipid 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 glycerolipid metabolic process phosphorus metabolic process lipid metabolic process piecemeal microautophagy of the nucleus microautophagy nucleophagy autophagy of peroxisome pexophagy establishment of protein localization protein targeting establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein localization protein targeting to vacuole intracellular protein transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi cytoplasm to vacuole targeting by the Cvt pathway cellular response to potassium ion starvation mitophagy autophagy of mitochondrion	organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane membrane phagophore assembly site phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane protein complex organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane membrane phagophore assembly site phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex 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 vacuolar membrane membrane-bounded organelle storage vacuole lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane Golgi membrane Golgi apparatus endomembrane system phosphatidylinositol 3-kinase complex, class III, type I endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle
D [auth E]	Nanobody binding S. cerevisiae Vps34	-	-	-
C [auth B]	Serine/threonine-protein kinase VPS15	protein binding binding ubiquitin binding ubiquitin-like protein binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding protein binding binding ubiquitin binding ubiquitin-like protein binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport phosphatidylinositol metabolic process glycerophospholipid 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 catabolic process autophagy process utilizing autophagic mechanism autophagy of peroxisome macroautophagy pexophagy cellular component organization organelle organization vacuole organization organelle inheritance vacuole inheritance cellular component organization or biogenesis establishment of protein localization protein targeting establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein localization protein targeting to vacuole intracellular protein transport transcription elongation by RNA polymerase II regulation of cellular process positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of biological process regulation of transcription elongation by RNA polymerase II biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein retention in Golgi apparatus cellular response to potassium ion starvation cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site vacuole-isolation membrane contact site nucleus-vacuole junction phagophore assembly site membrane membrane phagophore assembly site membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site vacuole-isolation membrane contact site nucleus-vacuole junction phagophore assembly site membrane membrane phagophore assembly site phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex 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 vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane Golgi membrane Golgi apparatus endomembrane system phosphatidylinositol 3-kinase complex, class III, type I endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle late endosome
B [auth C]	Phosphatidylinositol 3-kinase VPS34	phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein protein kinase activity	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process glycerophospholipid metabolic process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport 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 autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis process utilizing autophagic mechanism import into cell endocytosis establishment of protein localization protein transport macromolecule localization intracellular protein localization autophagy of peroxisome pexophagy cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication phosphatidylinositol-mediated signaling signal transduction transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cellular response to potassium ion starvation cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation	cellular anatomical structure membrane nucleus-vacuole junction organelle membrane contact site organelle intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane phagophore assembly site phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane protein complex cellular anatomical structure membrane nucleus-vacuole junction organelle membrane contact site organelle intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane phagophore assembly site phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex 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 vacuolar membrane membrane-bounded organelle storage vacuole lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle Golgi membrane Golgi apparatus phosphatidylinositol 3-kinase complex, class III, type I peroxisome microbody endosome membrane cytoplasmic vesicle membrane vesicle membrane
A	Vacuolar protein sorting-associated protein 38	protein binding binding SNARE binding	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport catabolic process macroautophagy autophagy metabolic process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism membrane organization protein-containing complex organization membrane fusion organelle membrane fusion cellular component organization cellular component biogenesis vesicle organization organelle fusion organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular component organization or biogenesis vesicle fusion phosphatidylinositol metabolic process glycerophospholipid 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 glycerolipid metabolic process phosphorus metabolic process lipid metabolic process establishment of protein localization protein transport macromolecule localization intracellular protein localization cellular response to potassium ion starvation cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation	vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane fungal-type vacuole membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle Golgi membrane Golgi apparatus endosome membrane cytoplasmic vesicle membrane vesicle membrane phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth D]	IPR007243	Atg6/Beclin	Family
E [auth D]	IPR041691	Atg6/beclin, coiled-coil domain	Domain
E [auth D]	IPR038274	Atg6/Beclin C-terminal domain superfamily	Homologous Superfamily
E [auth D]	IPR040455	Atg6, BARA domain	Domain
C [auth B]	IPR016024	Armadillo-type fold	Homologous Superfamily
C [auth B]	IPR021133	HEAT, type 2	Repeat
C [auth B]	IPR011989	Armadillo-like helical	Homologous Superfamily
C [auth B]	IPR000719	Protein kinase domain	Domain
C [auth B]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C [auth B]	IPR055231	PIK3R4-like, middle domain	Domain
C [auth B]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C [auth B]	IPR001680	WD40 repeat	Repeat
C [auth B]	IPR045162	Serine/threonine-protein kinase Vps15-like	Family
C [auth B]	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B [auth C]	IPR015433	Phosphatidylinositol 3-/4-kinase	Family
B [auth C]	IPR016024	Armadillo-type fold	Homologous Superfamily
B [auth C]	IPR057756	Phosphatidylinositol 3-kinase type3/VPS34-like	Domain
B [auth C]	IPR002420	C2 phosphatidylinositol 3-kinase-type domain	Domain
B [auth C]	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
B [auth C]	IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain	Domain
B [auth C]	IPR018936	Phosphatidylinositol 3-/4-kinase, conserved site	Conserved Site
B [auth C]	IPR042236	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily	Homologous Superfamily
B [auth C]	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
B [auth C]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth C]	IPR035892	C2 domain superfamily	Homologous Superfamily
B [auth C]	IPR008290	Phosphatidylinositol 3-kinase, Vps34 type	Family
A	IPR040939	Vacuolar protein sorting 38	Family