2Z0D

The crystal structure of human Atg4B- LC3(1-120) complex

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)
B	d2z0db_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d2z0da1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Autophagin-like	Cysteine protease ATG4B	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)
B	SCOP2 Family	GABARAP-like	8031097	4000970	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ubiquitin-like	8043475	3000157	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8033717	3001808	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)
B	PF02991	e2z0dB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF02991	ECOD (1.6)
A	PF03416	e2z0dA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF03416	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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
B	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain
A	PF03416	Peptidase family C54 (Peptidase_C54)	Peptidase family C54	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Microtubule-associated proteins 1A/1B light chain 3B	protein binding binding protein domain specific binding cytoskeletal protein binding tubulin binding amide binding ceramide binding sphingolipid binding lipid binding phosphatidylethanolamine binding phospholipid binding microtubule binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein binding binding protein domain specific binding cytoskeletal protein binding tubulin binding amide binding ceramide binding sphingolipid binding lipid binding phosphatidylethanolamine binding phospholipid binding microtubule binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular component disassembly catabolic process macroautophagy protein-containing complex organization cellular metabolic process autophagy protein-containing complex disassembly cellular catabolic process cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism cellular component disassembly catabolic process macroautophagy protein-containing complex organization cellular metabolic process autophagy protein-containing complex disassembly cellular catabolic process cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism 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 response to starvation autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly multicellular organismal process regulation of body fluid levels secretion by tissue secretion transport biological regulation mucus secretion establishment of localization localization body fluid secretion regulation of biological quality cellular localization establishment of localization in cell regulation of localization regulation of biological process regulation of transport regulation of mucus secretion positive regulation of biological process regulation of secretion positive regulation of secretion positive regulation of transport positive regulation of mucus secretion positive regulation of multicellular organismal process regulation of multicellular organismal process mitophagy organelle disassembly autophagy of mitochondrion mitochondrion organization	cellular anatomical entity endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane axoneme ciliary plasm cilium cytoplasmic region cellular anatomical entity endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle mitochondrial membrane organelle envelope mitochondrial envelope organelle membrane cytosol somatodendritic compartment dendrite dendritic tree neuron projection cytoplasmic vesicle intracellular vesicle vesicle vacuole autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle cell body neuronal cell body axon autolysosome lytic vacuole secondary lysosome lysosome protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex
A	Cysteine protease ATG4B	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity cysteine-type peptidase activity cysteine-type endopeptidase activity scaffold protein binding protein binding binding protein-phosphatidylethanolamide deconjugating activity	developmental process ear development sensory organ development animal organ development tissue development otolith mineralization otolith development otolith mineralization completed early in development inner ear development anatomical structure development biomineral tissue development cellular catabolic process catabolic process macroautophagy developmental process ear development sensory organ development animal organ development tissue development otolith mineralization otolith development otolith mineralization completed early in development inner ear development anatomical structure development biomineral tissue development cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism organic substance metabolic process organonitrogen compound metabolic process macromolecule modification protein delipidation primary metabolic process protein metabolic process macromolecule metabolic process protein modification process autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis microautophagy 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 cellular component disassembly mitophagy organelle disassembly autophagy of mitochondrion mitochondrion organization proteolysis protein localization to phagophore assembly site	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytoplasmic vesicle intracellular vesicle vesicle vacuolar membrane autophagosome membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytoplasmic vesicle intracellular vesicle vesicle vacuolar membrane autophagosome membrane membrane vacuole autophagosome bounding membrane of organelle organelle membrane cytosol endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR046792	Peptidase C54, catalytic domain	Domain
A	IPR005078	Peptidase C54	Family
A	IPR046793	Cysteine protease ATG4, F-type LIR motif	Conserved Site
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y4P1	allergic rhinitis breast carcinoma ovarian cancer asthma inflammatory bowel disease psoriasis brain glioma osteosarcoma

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 R01GM133198.