4GSK | pdb_00004gsk

Crystal structure of an Atg7-Atg10 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)
D [auth Z]	SCOP2B Superfamily	Type III secretory system chaperone-like	8052662	3000727	SCOP2B (2022-06-29)
C [auth Y]	SCOP2B Superfamily	Type III secretory system chaperone-like	8052662	3000727	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8052657	3001105	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8052658	3001105	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8052658	3001105	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8052657	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 [auth Z]	Glyco_hydro_31_2nd	e4gskZ1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
C [auth Y]	GFO_IDH_MocA	e4gskY1	A: alpha bundles	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: GFO_IDH_MocA	ECOD (develop294)
B	ClpB_D2-small	e4gskB1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: ClpB_D2-small	ECOD (develop294)
A	ClpB_D2-small	e4gskA1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: ClpB_D2-small	ECOD (develop294)

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 [auth Y], D [auth Z]	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 [auth Y], D [auth Z]	Ubiquitin-like-conjugating enzyme ATG10	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity Atg12 transferase activity transferase activity catalytic activity	macromolecule modification metabolic process cellular process 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 catabolic process macroautophagy autophagy process utilizing autophagic mechanism macromolecule modification metabolic process cellular process 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 catabolic process macroautophagy autophagy process utilizing autophagic mechanism 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 piecemeal microautophagy of the nucleus microautophagy	phagophore assembly site membrane cellular anatomical structure intracellular anatomical structure membrane phagophore assembly site cytoplasm
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 [auth Y], D [auth Z]	IPR007135	Ubiquitin-like-conjugating enzyme Atg3/Atg10	Family
C [auth Y], D [auth Z]	IPR016524	Ubiquitin-like-conjugating enzyme 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.