2DYM | pdb_00002dym

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) 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)
A	SCOP2B Superfamily	Ubiquitin-like	8090301	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8090302	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8090301	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8090302	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8090302	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8090302	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8090301	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	APG5_1st	e2dymA2	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
A	APG5_2nd	e2dymA3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
A	KOG2976	e2dymA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
C	APG5_1st	e2dymC3	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
C	APG5_2nd	e2dymC2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
C	KOG2976	e2dymC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
E	APG5_1st	e2dymE3	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
E	APG5_2nd	e2dymE2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
E	KOG2976	e2dymE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
G	APG5_1st	e2dymG3	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
G	APG5_2nd	e2dymG2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
G	KOG2976	e2dymG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	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)
E	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
E	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
G	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
G	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, E, G	PF20637	Autophagy protein ATG5, alpha-helical bundle region (ATG5_HBR)	Autophagy protein ATG5, alpha-helical bundle region	Autophagy protein ATG5 is involved in autophagic vesicle formation. It is conjugated with ATG12, acting as an E3-like ubiquitin enzyme required for lipidation of ATG8 family proteins and their association to the vesicle membranes. ATG5 comprises two ...	Autophagy protein ATG5 is involved in autophagic vesicle formation. It is conjugated with ATG12, acting as an E3-like ubiquitin enzyme required for lipidation of ATG8 family proteins and their association to the vesicle membranes. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain. This domain represents the alpha-helical bundle region (HBR) of AT5 which consists of three alpha helices [1,2]. This region contains the Lys residue required for conjugation with ATG12 [1].	Domain
A, C, E, G	PF20638	Autophagy protein ATG5, UblA domain (ATG5_UblA)	Autophagy protein ATG5, UblA domain	This is the N-terminal ubiquitin-like domain, termed UblA, from autophagy protein ATG5 [1,2]. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain (HBR). Both UblA and UblB comprise a five-stranded sheet and two-he ...	This is the N-terminal ubiquitin-like domain, termed UblA, from autophagy protein ATG5 [1,2]. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain (HBR). Both UblA and UblB comprise a five-stranded sheet and two-helices.	Domain
A, C, E, G	PF04106	Autophagy protein ATG5, UblB domain (ATG5_UblB)	Autophagy protein ATG5, UblB domain	ATG5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [1]. ATG5 is conjugated to ATG12; this conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 famil ...	ATG5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [1]. ATG5 is conjugated to ATG12; this conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 family, and therefore autophagosome formation [2]. ATG5 comprises N- and C-terminal ubiquitin-like domains (UblA and UblB) that flank the helical-rich region (HBR). This is the UblB domain, found at the C-terminal [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Autophagy protein 5	protein binding binding cargo receptor ligand activity hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function 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 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 aggrephagy protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting establishment of protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway localization 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 cellular response to potassium ion starvation mitophagy autophagy of mitochondrion	organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane intracellular anatomical structure phagophore cytoplasm cytosol phagophore assembly site membrane phagophore assembly site protein-containing complex catalytic complex Atg12-Atg5-Atg16 complex organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane intracellular anatomical structure phagophore cytoplasm cytosol phagophore assembly site membrane phagophore assembly site protein-containing complex catalytic complex Atg12-Atg5-Atg16 complex transferase complex membrane-bounded organelle intracellular organelle vacuole autophagosome intracellular membrane-bounded organelle nucleus
B, D, F, H	Autophagy protein 16	protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein binding binding	catabolic process macroautophagy autophagy cellular process 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 catabolic process macroautophagy autophagy cellular process 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 protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting establishment of protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway localization 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 piecemeal microautophagy of the nucleus microautophagy nucleophagy	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm organelle membrane contact site organelle vacuole-isolation membrane contact site phagophore cytosol phagophore assembly site membrane membrane protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm organelle membrane contact site organelle vacuole-isolation membrane contact site phagophore cytosol phagophore assembly site membrane membrane phagophore assembly site membrane-bounded organelle intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR048318	Autophagy protein ATG5, UblB domain	Domain
A, C, E, G	IPR007239	Autophagy-related protein 5	Family
A, C, E, G	IPR042527	Autophagy protein Atg5, UblA domain superfamily	Homologous Superfamily
A, C, E, G	IPR048940	Autophagy protein ATG5, alpha-helical bundle region	Domain
A, C, E, G	IPR042526	Autophagy protein Atg5, helix rich domain	Homologous Superfamily
A, C, E, G	IPR048939	Autophagy protein ATG5, UblA domain	Domain
B, D, F, H	IPR013923	Autophagy-related protein 16 domain	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.