3M95

Crystal structure of autophagy-related protein Atg8 from the silkworm Bombyx mori

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3m95a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)
B	d3m95b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)
B	d3m95b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Silk moth (Bombyx mori ) [TaxId: 7091 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GABARAP-like	8068225	4000970	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ubiquitin-like	8068226	3000157	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8068226	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	Atg8	e3m95A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
B	Atg8	e3m95B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	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)
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
A, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Autophagy related protein Atg8	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding signaling receptor binding GABA receptor binding	cellular catabolic process catabolic process cellular metabolic process autophagy cellular process metabolic process autophagy of mitochondrion 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 catabolic process catabolic process cellular metabolic process autophagy cellular process metabolic process autophagy of mitochondrion 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 macroautophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol vacuolar membrane membrane-bounded organelle autophagosome membrane membrane vacuole intracellular membrane-bounded organelle autophagosome intracellular organelle bounding membrane of organelle organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol vacuolar membrane membrane-bounded organelle autophagosome membrane membrane vacuole intracellular membrane-bounded organelle autophagosome intracellular organelle bounding membrane of organelle organelle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.