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)
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)
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)
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)
A [auth D]	ATG7_N_1st	e3vx8D2	A: a/b three-layered sandwiches	X: Atg7 N-terminal domain-like	H: N-terminal domain in E1 enzyme Atg7 (From Topology)	T: N-terminal domain in E1 enzyme Atg7	F: ATG7_N_1st	ECOD (1.6)
A [auth D]	ATG7_N_2nd	e3vx8D1	A: a/b three-layered sandwiches	X: Atg7 N-terminal domain-like	H: N-terminal domain in E1 enzyme Atg7 (From Topology)	T: N-terminal domain in E1 enzyme Atg7	F: ATG7_N_2nd	ECOD (1.6)
B [auth A]	ATG7_N_1st	e3vx8A2	A: a/b three-layered sandwiches	X: Atg7 N-terminal domain-like	H: N-terminal domain in E1 enzyme Atg7 (From Topology)	T: N-terminal domain in E1 enzyme Atg7	F: ATG7_N_1st	ECOD (1.6)
B [auth A]	ATG7_N_2nd	e3vx8A3	A: a/b three-layered sandwiches	X: Atg7 N-terminal domain-like	H: N-terminal domain in E1 enzyme Atg7 (From Topology)	T: N-terminal domain in E1 enzyme Atg7	F: ATG7_N_2nd	ECOD (1.6)
C [auth B]	Autophagy_act_C	e3vx8B1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: Autophagy_act_C	ECOD (1.6)
D [auth C]	Autophagy_act_C	e3vx8C1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: Autophagy_act_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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 Atg8 activating enzyme activity catalytic activity ligase activity ATP-dependent activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to fungus defense response to other organism response to stress response to external biotic stimulus response to fungus catabolic process autophagy cellular process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to fungus defense response to other organism response to stress response to external biotic stimulus response to fungus catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization lipoprotein biosynthetic process lipoprotein metabolic process primary metabolic process macromolecule biosynthetic process protein lipidation biosynthetic process macromolecule modification protein metabolic process macromolecule metabolic process protein modification process developmental process multicellular organismal process plant organ development plant organ senescence multicellular organism development anatomical structure development leaf development leaf senescence shoot system development phyllome development system development	cellular anatomical structure intracellular anatomical structure cytoplasm
C [auth B], D [auth C]	Autophagy-related protein 3	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity	catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization	cellular anatomical structure intracellular anatomical structure cytoplasm

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	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.