2ZPN | pdb_00002zpn

The crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412-415) complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2zpna_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2zpnb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2zpnc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d2zpnd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8068236	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8068236	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8068236	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8068236	3000157	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	Atg8	e2zpnA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
B	Atg8	e2zpnB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
C	Atg8	e2zpnC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
D	Atg8	e2zpnD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Autophagy-related protein 8	phosphatidylethanolamine binding binding phospholipid binding lipid binding protein tag activity molecular tag activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism 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 regulation of biological process regulation of cellular process biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy regulation of metabolic process autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly piecemeal microautophagy of the nucleus microautophagy nucleophagy localization protein-containing complex localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting to vacuole involved in autophagy protein targeting establishment of protein localization to vacuole cellular macromolecule localization establishment of localization in cell protein targeting to vacuole intracellular transport protein localization to vacuole establishment of localization establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle vacuolar transport intracellular protein transport endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport vesicle-mediated transport autophagy of mitochondrion cytoplasm to vacuole targeting by the Cvt pathway regulation of cellular component organization membrane invagination regulation of membrane invagination mitophagy lipid storage membraneless organelle assembly lipid droplet formation lipid droplet organization nutrient storage protein localization to phagophore assembly site reticulophagy	organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope mitochondrial envelope cytoplasm organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope mitochondrial envelope cytoplasm organelle membrane cytosol vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle fungal-type vacuole membrane autophagosome autophagosome membrane lipid droplet membraneless organelle intracellular membraneless organelle intracellular vesicle Cvt vesicle membrane cytoplasmic vesicle membrane Cvt vesicle vesicle membrane cytoplasmic vesicle vesicle phagophore assembly site
E, F, G, H	Saccharomyces cerevisiae Atg19(412-415)	protein-macromolecule adaptor activity molecular adaptor activity	localization protein-containing complex localization cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical localization protein-containing complex localization cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress vesicle organization cellular component organization organelle organization cellular component organization or biogenesis autophagy process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization protein transport cellular macromolecule localization macromolecule localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane membrane phagophore assembly site protein-containing complex Cvt complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR024543	Autophagy protein Atg19/Atg34, C-terminal	Domain

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.