Annotations: 6KBM

Crystal structure of Vac8 bound to Atg13

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ATP-synt	e6kbmA1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: ATP-synt	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00514	Armadillo/beta-catenin-like repeat (Arm)	Armadillo/beta-catenin-like repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Autophagy-related protein 13	armadillo repeat domain binding protein binding binding protein domain specific binding lipid binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	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 cellular process response to starvation establishment of protein localization cellular localization 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 cellular process response to starvation establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway cellular component biogenesis cellular component organization vesicle organization localization cellular component assembly establishment of localization in cell cellular component organization or biogenesis intracellular protein localization process utilizing autophagic mechanism protein targeting to vacuole organelle assembly intracellular transport protein localization to vacuole establishment of localization organelle organization establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization vacuolar transport Cvt vesicle assembly intracellular protein transport autophagosome assembly catabolic process vacuole organization macroautophagy autophagy autophagosome organization metabolic process piecemeal microautophagy of the nucleus microautophagy nucleophagy regulation of localization regulation of biological process regulation of cellular process regulation of cellular localization biological regulation protein targeting to vacuole involved in autophagy autophagy of mitochondrion mitophagy positive regulation of autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of metabolic process positive regulation of cellular process protein localization to phagophore assembly site	organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex intracellular anatomical structure catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm transferase complex cytosol organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex intracellular anatomical structure catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm transferase complex cytosol vacuolar membrane membrane-bounded organelle membrane PAS complex membrane protein complex vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle membrane phagophore assembly site
A	Vacuolar protein 8	protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein binding binding	cellular component biogenesis cellular component organization organelle localization by membrane tethering localization cellular component assembly organelle localization cellular process cellular component organization or biogenesis membrane docking nucleus-vacuole junction assembly establishment of protein localization cellular localization transport protein targeting cellular component biogenesis cellular component organization organelle localization by membrane tethering localization cellular component assembly organelle localization cellular process cellular component organization or biogenesis membrane docking nucleus-vacuole junction assembly establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway vesicle organization establishment of localization in cell intracellular protein localization process utilizing autophagic mechanism protein targeting to vacuole organelle assembly intracellular transport protein localization to vacuole establishment of localization organelle organization establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization vacuolar transport Cvt vesicle assembly intracellular protein transport autophagosome assembly catabolic process vacuole organization macroautophagy autophagy autophagosome organization metabolic process piecemeal microautophagy of the nucleus microautophagy nucleophagy protein-containing complex localization primary metabolic process lipid metabolic process autophagy of peroxisome pexophagy organelle fusion vacuole fusion vacuole fusion, non-autophagic ribophagy organelle inheritance vacuole inheritance protein localization to membrane raft localization within membrane protein localization to membrane establishment of organelle localization lipophagy protein localization to phagophore assembly site	cellular anatomical structure membrane nucleus-vacuole junction organelle membrane contact site organelle membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope cellular anatomical structure membrane nucleus-vacuole junction organelle membrane contact site organelle membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane cytoplasm cytosol membrane microdomain membrane raft vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle fungal-type vacuole membrane nuclear outer membrane organelle outer membrane nuclear outer membrane-endoplasmic reticulum membrane network outer membrane Myo2p-Vac17p-Vac8p transport complex protein-containing complex phagophore assembly site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR036570	HORMA domain superfamily	Homologous Superfamily
B	IPR040182	Autophagy-related protein 13	Family
B	IPR018731	Autophagy-related protein 13, N-terminal	Domain
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR000225	Armadillo	Repeat
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR045156	Vacuolar protein 8	Family

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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.

6KBM | pdb_00006kbm

Crystal structure of Vac8 bound to Atg13

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage