3VX8 | pdb_00003vx8

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 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)
B [auth A]	SCOP2 Family	Atg7 N-terminal domain-like	8045561	4004534	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	JAB1/MPN domain-like	8052656	3001105	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	JAB1/MPN domain-like	8052655	3001105	SCOP2 (2022-06-29)
A [auth D]	SCOP2B Superfamily	JAB1/MPN domain-like	8052655	3001105	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	JAB1/MPN domain-like	8052656	3001105	SCOP2B (2022-06-29)
C [auth B]	SCOP2 Family	Atg3-like	8045328	4004412	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Superfamily	Type III secretory system chaperone-like	8045324	3000727	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)
B [auth A]		e3vx8A2	A: POZ domain	X: POZ domain	H: POZ domain	T: PolyA_pol	F:	ECOD (20:10:01)
A [auth D]		e3vx8D1	A: Thioredoxin-like	X: Thioredoxin-like	H: Thioredoxin-like	T:	F:	ECOD (20:10:01)
D [auth C]		e3vx8C1	A: Ribosomal protein L31e-like	X: Reductive activator for corrinoid/iron-sulfur protein second domain	H: Reductive activator for corrinoid/iron-sulfur protein second domain	T: SIS	F:	ECOD (20:10:01)
C [auth B]		e3vx8B1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Autophagy_act_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.140.100	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B [auth A]	3.40.140.70	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
A [auth D]	3.40.140.100	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
A [auth D]	3.40.140.70	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A]	PF16420	Ubiquitin-like modifier-activating enzyme ATG7 N-terminus (ATG7_N)	Ubiquitin-like modifier-activating enzyme ATG7 N-terminus	This is the N-terminal domain of Ubiquitin-like modifier-activating enzyme ATG7. In Arabidopsis this domain binds the E2 enzymes ATG10 and ATG3 [1].	Domain
C [auth B], D [auth C]	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 [auth D], B [auth A]	Ubiquitin-like modifier-activating enzyme atg7	ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein catalytic activity Atg12 activating enzyme activity ligase activity ATP-dependent activity Atg8 activating enzyme 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 developmental process multicellular organismal process plant organ development 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 developmental process multicellular organismal process plant organ development regulation of biological process plant organ senescence regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of leaf senescence multicellular organism development negative regulation of leaf senescence anatomical structure development leaf development leaf senescence shoot system development phyllome development system development defense response to fungus biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus response to fungus response to external biotic stimulus response to biotic stimulus 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 localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization macromolecule modification primary metabolic process 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 mitophagy autophagy of mitochondrion	cellular anatomical structure intracellular anatomical structure cytoplasm phagophore assembly site
C [auth B], D [auth C]	Autophagy-related protein 3	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	carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy polysaccharide catabolic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process process utilizing autophagic mechanism nucleophagy 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 localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol phagophore assembly site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A]	IPR042522	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1	Homologous Superfamily
A [auth D], B [auth A]	IPR045886	ThiF/MoeB/HesA family	Family
A [auth D], B [auth A]	IPR006285	Ubiquitin-like modifier-activating enzyme Atg7	Family
A [auth D], B [auth A]	IPR000594	THIF-type NAD/FAD binding fold	Domain
A [auth D], B [auth A]	IPR032197	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal	Domain
A [auth D], B [auth A]	IPR042523	Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2	Homologous Superfamily
A [auth D], B [auth A]	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily
C [auth B], D [auth C]	IPR007135	Ubiquitin-like-conjugating enzyme Atg3/Atg10	Family

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.