4NAW

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4nawa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4nawe_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d4nawi_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d4nawm_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	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	8088977	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8088977	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8088977	3000157	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ubiquitin-like	8088977	3000157	SCOP2B (2022-06-29)
N	SCOP2 Family	ATG5-like	8045342	4004425	SCOP2 (2022-06-29)
N	SCOP2 Superfamily	Ubiquitin-like	8090297	3000157	SCOP2 (2022-06-29)
N	SCOP2 Superfamily	Ubiquitin-like	8090298	3000157	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8090298	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8090297	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8090297	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8090298	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8090298	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8090297	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2B (2022-06-29)
O	SCOP2 Family	ATG16-like	8051035	4007169	SCOP2 (2022-06-29)
O	SCOP2 Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2 (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	PF04110	e4nawA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04110	ECOD (1.6)
E	PF04110	e4nawE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04110	ECOD (1.6)
I	PF04110	e4nawI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04110	ECOD (1.6)
M	PF04110	e4nawM1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04110	ECOD (1.6)
N	PF20637	e4nawN6	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: PF20637	ECOD (1.6)
N	PF04106	e4nawN5	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04106	ECOD (1.6)
N	PF20638	e4nawN2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF20638	ECOD (1.6)
B	PF20637	e4nawB8	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: PF20637	ECOD (1.6)
B	PF04106	e4nawB7	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04106	ECOD (1.6)
B	PF20638	e4nawB6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF20638	ECOD (1.6)
F	PF20637	e4nawF8	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: PF20637	ECOD (1.6)
F	PF04106	e4nawF7	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04106	ECOD (1.6)
F	PF20638	e4nawF6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF20638	ECOD (1.6)
J	PF20637	e4nawJ8	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: PF20637	ECOD (1.6)
J	PF04106	e4nawJ7	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF04106	ECOD (1.6)
J	PF20638	e4nawJ6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF20638	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)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
I	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
M	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
N	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
N	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
N	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	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)
B	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
F	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
J	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
J	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
J	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E, I, M	PF04110	Ubiquitin-like autophagy protein Apg12 (APG12)	Ubiquitin-like autophagy protein Apg12	In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukar ...	In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukaryotes. It was first discovered in yeast during systematic analyses of the apg mutants defective in autophagy. Covalent attachment of Apg12-Apg5 is essential for autophagy [2,3,4].	Domain
B, F, J, N	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
B, F, J, N	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
B, F, J, N	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
C, G, K, O	PF08614	Autophagy protein 16 (ATG16) (ATG16)	Autophagy protein 16 (ATG16)	-	Coiled-coil
D, H, L, P	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E, I, M	Ubiquitin-like protein ATG12	-	cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production organic substance metabolic process cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process type I interferon production negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus response to stimulus regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus negative regulation of response to stimulus immune response response to other organism defense response regulation of innate immune response negative regulation of immune response defense response to symbiont response to external stimulus regulation of response to stimulus negative regulation of immune system process immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response regulation of defense response to virus response to virus defense response to virus negative regulation of defense response to virus nucleophagy regulation of cellular component organization regulation of autophagosome maturation protein-containing complex disassembly regulation of autophagy regulation of protein-containing complex disassembly autophagosome maturation cellular component disassembly protein-containing complex organization regulation of catabolic process regulation of organelle organization regulation of macroautophagy regulation of cellular catabolic process viral gene expression regulation of viral translation regulation of viral process positive regulation of viral process viral process positive regulation of biological process positive regulation of viral translation viral translation	protein-containing complex intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle membrane protein-containing complex intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle membrane intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle organelle membrane endocytic vesicle cytosol phagophore assembly site membrane phagophore assembly site nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, F, J, N	Autophagy protein 5	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity Atg8-family ligase activity ubiquitin-like protein ligase activity transferase activity catalytic activity	response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production organic substance metabolic process cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production organic substance metabolic process cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process type I interferon production cellular metabolic process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production developmental process thymic T cell selection cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation negative thymic T cell selection anatomical structure development T cell differentiation negative T cell selection T cell selection leukocyte differentiation antigen processing and presentation antigen processing and presentation of endogenous antigen negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process organonitrogen compound metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular catabolic process catabolic process autophagy process utilizing autophagic mechanism macroautophagy aggrephagy regulation of body fluid levels secretion by tissue secretion transport mucus secretion establishment of localization localization body fluid secretion regulation of biological quality regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus regulation of response to external stimulus response to biotic stimulus regulation of defense response to virus response to stress regulation of response to stress response to external biotic stimulus response to virus negative regulation of response to stimulus response to other organism defense response response to external stimulus defense response to symbiont defense response to virus regulation of response to stimulus negative regulation of response to external stimulus defense response to other organism negative regulation of defense response negative regulation of defense response to virus response to fungus response to iron(II) ion response to metal ion response to iron ion response to inorganic substance reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization organelle assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly organelle organization regulation of organelle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of striated muscle cell apoptotic process apoptotic process programmed cell death regulation of calcium ion transport regulation of localization intracellular calcium ion homeostasis calcium ion transport monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport inorganic ion transmembrane transport inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis cellular localization inorganic ion homeostasis homeostatic process monoatomic ion transmembrane transport calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis monoatomic ion transport intracellular chemical homeostasis regulation of metal ion transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion cellular homeostasis regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport regulation of autophagosome maturation protein-containing complex disassembly regulation of autophagy regulation of protein-containing complex disassembly autophagosome maturation cellular component disassembly protein-containing complex organization regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process organonitrogen compound catabolic process protein catabolic process macromolecule catabolic process chaperone-mediated autophagy organic substance catabolic process protein-DNA complex organization chromatin organization autophagic cell death regulation of autophagic cell death negative regulation of autophagic cell death regulation of immune effector process regulation of immune system process cytokine production involved in immune response production of molecular mediator of immune response regulation of cytokine production involved in immune response immune response immune effector process regulation of production of molecular mediator of immune response cellular response to stimulus response to nutrient levels cellular response to nitrogen levels cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to starvation ear development sensory organ development inner ear development animal organ development otolith development autophagosome assembly vacuole organization autophagosome organization innate immune response regulation of innate immune response negative regulation of immune response negative regulation of immune system process regulation of immune response negative regulation of innate immune response nucleophagy response to fluoride cellular response to chemical stimulus response to nitrosative stress cellular response to nitrosative stress cellular response to chemical stress establishment of localization in cell viral gene expression regulation of viral translation regulation of viral process positive regulation of viral process viral process positive regulation of biological process positive regulation of viral translation viral translation heart process system process circulatory system process heart contraction blood circulation regulation of tube diameter regulation of tube size vascular process in circulatory system blood vessel diameter maintenance vasodilation regulation of anatomical structure size ventricular cardiac muscle cell differentiation cardiac muscle cell development muscle cell differentiation striated muscle tissue development muscle structure development multicellular organism development muscle cell development muscle tissue development cardiac cell development system development heart development cardiac muscle tissue development cardiac muscle cell differentiation tissue development ventricular cardiac muscle cell development cardiocyte differentiation circulatory system development striated muscle cell differentiation blood vessel remodeling tissue remodeling import into cell negative regulation of transport negative regulation of endocytosis vesicle-mediated transport negative regulation of phagocytosis phagocytosis regulation of endocytosis negative regulation of cellular component organization regulation of phagocytosis regulation of vesicle-mediated transport endocytosis regulation of mucus secretion regulation of secretion positive regulation of secretion positive regulation of transport positive regulation of mucus secretion positive regulation of multicellular organismal process mitophagy organelle disassembly autophagy of mitochondrion mitochondrion organization RNA metabolic process viral life cycle RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral RNA genome replication nucleobase-containing compound biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process negative stranded viral RNA replication viral genome replication organic cyclic compound biosynthetic process	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle intracellular non-membrane-bounded organelle cytoplasm non-membrane-bounded organelle cytosol organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site vacuole autophagosome intracellular membrane-bounded organelle intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle organelle membrane endocytic vesicle protein-containing complex catalytic complex transferase complex axon neuron projection phagophore assembly site membrane phagophore assembly site Atg12-Atg5-Atg16 complex
C, G, K, O	Autophagy-related protein 16-1	protein binding binding enzyme binding GTPase binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity identical protein binding	developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development pallium development developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development pallium development hippocampus development limbic system development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response xenophagy response to external stimulus response to biotic stimulus defense response to other organism response to stress response to external biotic stimulus microautophagy defense response to symbiont defense response to virus response to virus cellular biosynthetic process RNA metabolic process viral life cycle RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral RNA genome replication viral process organic substance biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process negative stranded viral RNA replication viral genome replication biosynthetic process organic cyclic compound biosynthetic process macromolecule metabolic process positive regulation of autophagy regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of cellular metabolic process positive regulation of cellular metabolic process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of metabolic process positive regulation of cellular process C-terminal protein amino acid modification organonitrogen compound metabolic process lipoprotein biosynthetic process lipoprotein metabolic process organonitrogen compound biosynthetic process protein lipidation macromolecule modification protein metabolic process protein modification process post-translational protein modification C-terminal protein lipidation protein localization to phagophore assembly site	organelle membrane contact site organelle vacuole-isolation membrane contact site cellular anatomical entity membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection organelle membrane contact site organelle vacuole-isolation membrane contact site cellular anatomical entity membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton intracellular non-membrane-bounded organelle cytoplasm non-membrane-bounded organelle endosome membrane endolysosome membrane intracellular vesicle lytic vacuole endomembrane system bounding membrane of organelle endolysosome vesicle membrane cytoplasmic vesicle vesicle lysosome vacuolar membrane membrane endosome vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane organelle membrane cytosol phagophore assembly site membrane phagophore assembly site sperm midpiece 9+2 motile cilium sperm flagellum motile cilium protein-containing complex catalytic complex Atg12-Atg5-Atg16 complex transferase complex autophagosome autophagosome membrane
D, H, L, P	Ubiquitin-like-conjugating enzyme ATG3	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 Atg12 transferase activity Atg8-family ligase activity ubiquitin-like protein ligase activity protein binding binding enzyme binding	cellular component organization organelle organization mitochondrial fragmentation involved in apoptotic process apoptotic mitochondrial changes cellular process apoptotic process cellular component organization or biogenesis cell death programmed cell death mitochondrion organization regulation of cellular process regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization organelle organization mitochondrial fragmentation involved in apoptotic process apoptotic mitochondrial changes cellular process apoptotic process cellular component organization or biogenesis cell death programmed cell death mitochondrion organization regulation of cellular process regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization regulation of biological process organelle assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly biological regulation regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly regulation of organelle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization autophagosome assembly catabolic process vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular catabolic process metabolic process process utilizing autophagic mechanism regulation of localization import into cell transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport localization negative regulation of phagocytosis negative regulation of cellular process phagocytosis regulation of endocytosis negative regulation of cellular component organization regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization endocytosis protein localization establishment of protein localization cellular localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization nucleophagy organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification 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 establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane protein targeting to membrane	protein-containing complex intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm cellular anatomical entity cytosol phagophore assembly site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E, I, M	IPR007242	Ubiquitin-like protein Atg12	Family
A, E, I, M	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, F, J, N	IPR048318	Autophagy protein ATG5, UblB domain	Domain
B, F, J, N	IPR007239	Autophagy-related protein 5	Family
B, F, J, N	IPR042526	Autophagy protein Atg5, helix rich domain	Homologous Superfamily
B, F, J, N	IPR048939	Autophagy protein ATG5, UblA domain	Domain
B, F, J, N	IPR042527	Autophagy protein Atg5, UblA domain superfamily	Homologous Superfamily
B, F, J, N	IPR048940	Autophagy protein ATG5, alpha-helical bundle region	Domain
C, G, K, O	IPR045160	Autophagy-related protein 16	Family
C, G, K, O	IPR019775	WD40 repeat, conserved site	Conserved Site
C, G, K, O	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C, G, K, O	IPR013923	Autophagy-related protein 16 domain	Domain
C, G, K, O	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C, G, K, O	IPR001680	WD40 repeat	Repeat
C, G, K, O	IPR020472	G-protein beta WD-40 repeat	Repeat
D, H, L, P	IPR007135	Ubiquitin-like-conjugating enzyme Atg3/Atg10	Family
D, H, L, P	IPR046962	Autophagy-related protein 3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, E, I, M	Pharos: O94817	juvenile dermatomyositis osteosarcoma psoriasis large cell medulloblastoma ovarian cancer lung cancer plasma cell myeloma
B, F, J, N	Pharos: Q9H1Y0	Lethargy ovarian cancer rheumatoid arthritis systemic sclerosis anemia spinocerebellar ataxia, autosomal recessive 25 lymphopenia acne primary biliary cholangitis cancer colorectal cancer gastric cancer inflammatory bowel disease lung cancer medulloblastoma Lethargy ovarian cancer rheumatoid arthritis systemic sclerosis anemia spinocerebellar ataxia, autosomal recessive 25 lymphopenia acne primary biliary cholangitis cancer colorectal cancer gastric cancer inflammatory bowel disease lung cancer medulloblastoma neurodegenerative disease ovarian neoplasm primitive neuroectodermal tumor ulcerative colitis Crohn disease gastric carcinoma large cell medulloblastoma myositis osteosarcoma plasma cell myeloma atypical teratoid rhabdoid tumor psoriasis systemic lupus erythematosus diffuse scleroderma drug-induced liver injury glioblastoma
C, G, K, O	Pharos: Q676U5	Crohn disease inflammatory bowel disease inflammatory bowel disease 10 ulcerative colitis allergic rhinitis colitis Crohn's colitis ileocolitis intestinal disease osteosarcoma rheumatoid arthritis atopic eczema common variable immunodeficiency Crohn's disease of large bowel nephrolithiasis Crohn disease inflammatory bowel disease inflammatory bowel disease 10 ulcerative colitis allergic rhinitis colitis Crohn's colitis ileocolitis intestinal disease osteosarcoma rheumatoid arthritis atopic eczema common variable immunodeficiency Crohn's disease of large bowel nephrolithiasis Pick disease tuberculosis bowel dysfunction open-angle glaucoma
D, H, L, P	Pharos: Q9NT62	atopic eczema myopathy psoriasis juvenile dermatomyositis osteosarcoma malignant mesothelioma ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.