4TQ0 | pdb_00004tq0

Crystal structure of human ATG5-ATG16N69

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ATG16 helical segment-like	8090299	3002426	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8090297	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8090298	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8090298	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8090297	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8090297	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8090298	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)
F		e4tq0F1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Flavodoxin_2	F:	ECOD (20:10:01)
D		e4tq0D1	A: Rubredoxin-like	X: Rubredoxin-related	H: Rubredoxin-related	T: Peptidase_M28	F:	ECOD (20:10:01)
B		e4tq0B1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: DNA_pol_A	F:	ECOD (20:10:01)
E		e4tq0E1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: DNA_pol_A	F:	ECOD (20:10:01)
C		e4tq0C1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Flavodoxin_2	F:	ECOD (20:10:01)
A		e4tq0A1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Flavodoxin_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	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)
C	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)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	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	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	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
B, D, F	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 cellular developmental process 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 cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization dendrite arborization dendrite morphogenesis cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection arborization neuron development cellular process pallium development hippocampus development limbic system development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis organelle organization cellular component assembly metabolic process process utilizing autophagic mechanism localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization cellular localization intracellular transport axonal transport axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process 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 virus response to virus regulation of growth regulation of cellular process developmental growth negative regulation of biological process regulation of cell morphogenesis negative regulation of growth negative regulation of dendrite extension regulation of biological process negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of developmental growth regulation of cellular component organization regulation of developmental process cell growth negative regulation of cellular process dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth developmental cell growth negative regulation of developmental process growth biological regulation regulation of dendrite extension regulation of cell growth RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative stranded viral RNA replication viral genome replication biosynthetic process viral RNA genome replication viral process macromolecule metabolic process positive regulation of autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of metabolic process positive regulation of cellular process C-terminal protein amino acid modification lipoprotein biosynthetic process lipoprotein metabolic 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 cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton membraneless organelle cytoplasm 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 synapse cell junction glutamatergic synapse protein-containing complex catalytic complex Atg12-Atg5-Atg16 complex transferase complex autophagosome autophagosome membrane axon neuron projection
A, C, E	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 negative regulation of biological process negative regulation of type I interferon production cytokine production 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 response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of type I interferon production cytokine production 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 macromolecule metabolic process gene expression macromolecule 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 regulation of postsynaptic membrane neurotransmitter receptor levels regulation of biological quality 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 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 catabolic process autophagy process utilizing autophagic mechanism macroautophagy piecemeal microautophagy of the nucleus microautophagy nucleophagy aggrephagy biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of body fluid levels secretion by tissue secretion transport mucus secretion establishment of localization body fluid secretion localization regulation of defense response regulation of response to biotic stimulus negative regulation of response to biotic stimulus regulation of response to external stimulus regulation of defense response to virus regulation of response to stress response to virus negative regulation of response to stimulus defense response to virus regulation of response to stimulus negative regulation of response to external stimulus 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 cellular localization intracellular transport axonal transport axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling postsynaptic modulation of chemical synaptic transmission regulation of cell communication 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 monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport 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 protein catabolic process macromolecule catabolic process chaperone-mediated autophagy positive regulation of autophagy positive regulation of biological process positive regulation of catabolic process positive regulation of metabolic process positive regulation of cellular process 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 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 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 positive regulation of organelle organization positive regulation of cellular component organization stress granule assembly membraneless organelle assembly positive regulation of cellular component biogenesis positive regulation of stress granule assembly regulation of stress granule assembly positive regulation of organelle assembly response to fluoride cellular response to chemical stimulus response to nitrosative stress cellular response to nitrosative stress cellular response to chemical stress viral gene expression regulation of viral translation regulation of viral process positive regulation of viral process viral 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 striated muscle cell 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 reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process mitophagy autophagy of mitochondrion RNA metabolic process viral life cycle nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative stranded viral RNA replication viral genome replication viral RNA genome replication	organelle membrane contact site cellular anatomical structure organelle mitochondria-associated endoplasmic reticulum membrane contact site membrane membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection organelle membrane contact site cellular anatomical structure organelle mitochondria-associated endoplasmic reticulum membrane contact site membrane membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton membraneless organelle cytoplasm cytosol synapse cell junction glutamatergic synapse 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 postsynapse phagophore phagophore assembly site membrane phagophore assembly site Atg12-Atg5-Atg16 complex Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR045160	Autophagy-related protein 16	Family
B, D, F	IPR019775	WD40 repeat, conserved site	Conserved Site
B, D, F	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
B, D, F	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, D, F	IPR013923	Autophagy-related protein 16 domain	Domain
B, D, F	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, D, F	IPR001680	WD40 repeat	Repeat
A, C, E	IPR048318	Autophagy protein ATG5, UblB domain	Domain
A, C, E	IPR007239	Autophagy-related protein 5	Family
A, C, E	IPR042526	Autophagy protein Atg5, helix rich domain	Homologous Superfamily
A, C, E	IPR048939	Autophagy protein ATG5, UblA domain	Domain
A, C, E	IPR042527	Autophagy protein Atg5, UblA domain superfamily	Homologous Superfamily
A, C, E	IPR048940	Autophagy protein ATG5, alpha-helical bundle region	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F	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
A, C, E	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 Crohn disease ulcerative colitis 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

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.