5YEC | pdb_00005yec

Crystal structure of Atg7CTD-Atg8-MgATP complex in form II

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)
D	d5yecd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5yecb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ubiquitin-like	8068236	3000157	SCOP2B (2022-06-29)
B	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)
C	V-set	e5yecC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
A	V-set	e5yecA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
D	V-set	e5yecD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
B	V-set	e5yecB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	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)
B	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, C	PF00899	ThiF family (ThiF)	ThiF family	This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3].	Domain
B, 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, C	Ubiquitin-like modifier-activating enzyme ATG7	ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein catalytic activity Atg12 activating enzyme activity ligase activity ATP-dependent activity Atg8 activating enzyme activity identical protein binding protein binding binding	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 autophagosome assembly catabolic process organelle assembly 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 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 piecemeal microautophagy of the nucleus microautophagy nucleophagy autophagy of mitochondrion establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway establishment of localization localization establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle macromolecule localization vacuolar transport intracellular protein localization protein targeting to vacuole intracellular protein transport macromolecule modification primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal mitophagy	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane cytosol extrinsic component of organelle membrane phagophore assembly site membrane extrinsic component of phagophore assembly site membrane phagophore assembly site membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane cytosol extrinsic component of organelle membrane phagophore assembly site membrane extrinsic component of phagophore assembly site membrane phagophore assembly site extrinsic component of membrane organelle membrane
B, 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 macromolecule localization protein-containing complex localization establishment of protein localization cellular localization transport protein targeting to vacuole involved in autophagy protein targeting establishment of protein localization to vacuole establishment of localization in cell intracellular protein localization protein targeting to vacuole intracellular transport protein localization to vacuole establishment of localization establishment of protein localization to organelle protein transport protein localization to organelle vacuolar transport intracellular protein transport endoplasmic reticulum to Golgi vesicle-mediated transport vesicle-mediated transport intercellular transport Golgi vesicle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR045886	ThiF/MoeB/HesA family	Family
A, C	IPR006285	Ubiquitin-like modifier-activating enzyme Atg7	Family
A, C	IPR042522	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1	Homologous Superfamily
A, C	IPR000594	THIF-type NAD/FAD binding fold	Domain
A, C	IPR032197	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal	Domain
A, C	IPR042523	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2	Homologous Superfamily
A, C	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily
B, D	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

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.