4NAW
Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
E | d4nawe_ | Alpha and beta proteins (a+b) | beta-Grasp (ubiquitin-like) | Ubiquitin-like | automated matches | automated matches | human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
I | d4nawi_ | Alpha and beta proteins (a+b) | beta-Grasp (ubiquitin-like) | Ubiquitin-like | automated matches | automated matches | human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
M | d4nawm_ | Alpha and beta proteins (a+b) | beta-Grasp (ubiquitin-like) | Ubiquitin-like | automated matches | automated matches | human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
A | d4nawa_ | Alpha and beta proteins (a+b) | beta-Grasp (ubiquitin-like) | Ubiquitin-like | automated matches | automated matches | 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) |
---|---|---|---|---|---|
E | SCOP2B Superfamily | Ubiquitin-like | 8088977 | 3000157 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Ubiquitin-like | 8088977 | 3000157 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | Ubiquitin-like | 8088977 | 3000157 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Ubiquitin-like | 8088977 | 3000157 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Ubiquitin-like | 8090298 | 3000157 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Ubiquitin-like | 8090297 | 3000157 | SCOP2B (2022-06-29) |
J | SCOP2B Superfamily | Ubiquitin-like | 8090298 | 3000157 | SCOP2B (2022-06-29) |
J | SCOP2B Superfamily | Ubiquitin-like | 8090297 | 3000157 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Ubiquitin-like | 8090297 | 3000157 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Ubiquitin-like | 8090298 | 3000157 | SCOP2B (2022-06-29) |
N | SCOP2 Family | ATG5-like | 8045342 | 4004425 | SCOP2 (2022-06-29) |
N | SCOP2 Superfamily | Ubiquitin-like | 8090297 | 3000157 | SCOP2 (2022-06-29) |
N | SCOP2 Superfamily | Ubiquitin-like | 8090298 | 3000157 | SCOP2 (2022-06-29) |
K | SCOP2B Superfamily | ATG16 helical segment-like | 8090299 | 3002426 | SCOP2B (2022-06-29) |
O | SCOP2 Family | ATG16-like | 8051035 | 4007169 | SCOP2 (2022-06-29) |
O | SCOP2 Superfamily | ATG16 helical segment-like | 8090299 | 3002426 | SCOP2 (2022-06-29) |
C | SCOP2B Superfamily | ATG16 helical segment-like | 8090299 | 3002426 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | ATG16 helical segment-like | 8090299 | 3002426 | 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) |
---|---|---|---|---|---|---|---|---|
E | APG12 | e4nawE1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG12 | ECOD (1.6) |
I | APG12 | e4nawI1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG12 | ECOD (1.6) |
M | APG12 | e4nawM1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG12 | ECOD (1.6) |
A | APG12 | e4nawA1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG12 | ECOD (1.6) |
B | APG5_1st | e4nawB8 | A: alpha bundles | X: Helical domain in autophagy protein 5 (From Topology) | H: Helical domain in autophagy protein 5 (From Topology) | T: Helical domain in autophagy protein 5 | F: APG5_1st | ECOD (1.6) |
B | APG5_2nd | e4nawB7 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG5_2nd | ECOD (1.6) |
B | KOG2976 | e4nawB6 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: KOG2976 | ECOD (1.6) |
J | APG5_1st | e4nawJ8 | A: alpha bundles | X: Helical domain in autophagy protein 5 (From Topology) | H: Helical domain in autophagy protein 5 (From Topology) | T: Helical domain in autophagy protein 5 | F: APG5_1st | ECOD (1.6) |
J | APG5_2nd | e4nawJ7 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG5_2nd | ECOD (1.6) |
J | KOG2976 | e4nawJ6 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: KOG2976 | ECOD (1.6) |
F | APG5_1st | e4nawF8 | A: alpha bundles | X: Helical domain in autophagy protein 5 (From Topology) | H: Helical domain in autophagy protein 5 (From Topology) | T: Helical domain in autophagy protein 5 | F: APG5_1st | ECOD (1.6) |
F | APG5_2nd | e4nawF7 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG5_2nd | ECOD (1.6) |
F | KOG2976 | e4nawF6 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: KOG2976 | ECOD (1.6) |
N | APG5_1st | e4nawN6 | A: alpha bundles | X: Helical domain in autophagy protein 5 (From Topology) | H: Helical domain in autophagy protein 5 (From Topology) | T: Helical domain in autophagy protein 5 | F: APG5_1st | ECOD (1.6) |
N | APG5_2nd | e4nawN5 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: APG5_2nd | ECOD (1.6) |
N | KOG2976 | e4nawN2 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: KOG2976 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF04110 | Ubiquitin-like autophagy protein Apg12 (APG12) | Ubiquitin-like autophagy protein Apg12 | In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukar ... | Domain | |
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 ... | Domain | |
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 ... | Domain | |
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 ... | Domain | |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR007242 | Ubiquitin-like protein Atg12 | Family | |
IPR029071 | Ubiquitin-like domain superfamily | Homologous Superfamily | |
IPR007135 | Ubiquitin-like-conjugating enzyme Atg3/Atg10 | Family | |
IPR046962 | Autophagy-related protein 3 | Family | |
IPR048318 | Autophagy protein ATG5, UblB domain | Domain | |
IPR007239 | Autophagy-related protein 5 | Family | |
IPR042526 | Autophagy protein Atg5, helix rich domain | Homologous Superfamily | |
IPR048939 | Autophagy protein ATG5, UblA domain | Domain | |
IPR042527 | Autophagy protein Atg5, UblA domain superfamily | Homologous Superfamily | |
IPR048940 | Autophagy protein ATG5, alpha-helical bundle region | Domain | |
IPR045160 | Autophagy-related protein 16 | Family | |
IPR019775 | WD40 repeat, conserved site | Conserved Site | |
IPR015943 | WD40/YVTN repeat-like-containing domain superfamily | Homologous Superfamily | |
IPR013923 | Autophagy-related protein 16 domain | Domain | |
IPR036322 | WD40-repeat-containing domain superfamily | Homologous Superfamily | |
IPR001680 | WD40 repeat | Repeat | |
IPR020472 | G-protein beta WD-40 repeat | Repeat |