4GSL | pdb_00004gsl

Crystal structure of an Atg7-Atg3 crosslinked complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8052658	3001105	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8052657	3001105	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8052657	3001105	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8052658	3001105	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)
D		e4gslD2	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Acetyltransf_1	F:	ECOD (20:10:01)
C		e4gslC2	A: POZ domain	X: POZ domain	H: POZ domain	T: Acetyltransf_1	F:	ECOD (20:10:01)
B		e4gslB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
A		e4gslA1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Phage tail protein-like	T: DUF4488	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF03987	Autophagocytosis associated protein, active-site domain (Autophagy_act_C)	Autophagocytosis associated protein, active-site domain	Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome ...	Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex [2].	Domain
A, B	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
A, B	PF16420	Ubiquitin-like modifier-activating enzyme ATG7 N-terminus (ATG7_N)	Ubiquitin-like modifier-activating enzyme ATG7 N-terminus	This is the N-terminal domain of Ubiquitin-like modifier-activating enzyme ATG7. In Arabidopsis this domain binds the E2 enzymes ATG10 and ATG3 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Autophagy-related protein 3	aminoacyltransferase activity Atg8-family conjugating enzyme activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity Atg8-family ligase activity ubiquitin-like protein ligase activity	carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy polysaccharide catabolic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process process utilizing autophagic mechanism autophagy of mitochondrion autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis 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 piecemeal microautophagy of the nucleus microautophagy nucleophagy establishment of protein localization to membrane localization within membrane protein targeting to membrane	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle phagophore cytosol phagophore assembly site
A, B	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR007135	Ubiquitin-like-conjugating enzyme Atg3/Atg10	Family
A, B	IPR045886	ThiF/MoeB/HesA family	Family
A, B	IPR006285	Ubiquitin-like modifier-activating enzyme Atg7	Family
A, B	IPR042522	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1	Homologous Superfamily
A, B	IPR000594	THIF-type NAD/FAD binding fold	Domain
A, B	IPR032197	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal	Domain
A, B	IPR042523	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2	Homologous Superfamily
A, B	IPR035985	Ubiquitin-activating enzyme-like	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.