8DAT
Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
I [auth J] | SCOP2B Superfamily | Ubiquitin-like | 8040187 | 3000157 | SCOP2B (2022-06-29) |
J [auth K] | SCOP2B Superfamily | Ubiquitin-like | 8040187 | 3000157 | SCOP2B (2022-06-29) |
K [auth L] | SCOP2B Superfamily | Ubiquitin-like | 8040187 | 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 | CDC48_N | e8datA4 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: CDC48_N | ECOD (1.6) |
A | CDC48 | e8datA5 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: CDC48 | ECOD (1.6) |
A | Vps4_C_C | e8datA1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: Vps4_C_C | ECOD (1.6) |
A | CDC48_2 | e8datA6 | A: a+b two layers | X: Cdc48 domain 2-like (From Topology) | H: Cdc48 domain 2-like (From Topology) | T: Cdc48 domain 2-like | F: CDC48_2 | ECOD (1.6) |
A | Sigma54_activat | e8datA2 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Sigma54_activat | ECOD (1.6) |
B | CDC48 | e8datB1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: CDC48 | ECOD (1.6) |
B | Vps4_C_C | e8datB2 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: Vps4_C_C | ECOD (1.6) |
B | Sigma54_activat | e8datB4 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Sigma54_activat | ECOD (1.6) |
C | CDC48_N | e8datC2 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: CDC48_N | ECOD (1.6) |
C | CDC48 | e8datC6 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: CDC48 | ECOD (1.6) |
C | Vps4_C_C | e8datC4 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: Vps4_C_C | ECOD (1.6) |
C | CDC48_2 | e8datC3 | A: a+b two layers | X: Cdc48 domain 2-like (From Topology) | H: Cdc48 domain 2-like (From Topology) | T: Cdc48 domain 2-like | F: CDC48_2 | ECOD (1.6) |
C | Sigma54_activat | e8datC1 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Sigma54_activat | ECOD (1.6) |
D | CDC48 | e8datD2 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: CDC48 | ECOD (1.6) |
D | Vps4_C_C | e8datD1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: Vps4_C_C | ECOD (1.6) |
D | Sigma54_activat | e8datD3 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Sigma54_activat | ECOD (1.6) |
E | CDC48 | e8datE3 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: CDC48 | ECOD (1.6) |
E | Vps4_C_C | e8datE1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: Vps4_C_C | ECOD (1.6) |
E | Sigma54_activat | e8datE4 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Sigma54_activat | ECOD (1.6) |
F | CDC48 | e8datF2 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: CDC48 | ECOD (1.6) |
F | Vps4_C_C | e8datF3 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: Vps4_C_C | ECOD (1.6) |
F | Sigma54_activat | e8datF1 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Sigma54_activat | ECOD (1.6) |
I [auth J] | ubiquitin_1 | e8datJ1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: ubiquitin_1 | ECOD (1.6) |
J [auth K] | ubiquitin_1 | e8datK1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: ubiquitin_1 | ECOD (1.6) |
K [auth L] | ubiquitin_1 | e8datL1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: ubiquitin_1 | ECOD (1.6) |
G | F_UNCLASSIFIED | e8datG1 | A: alpha arrays | X: C-terminal domain of Npl4 (From Topology) | H: C-terminal domain of Npl4 (From Topology) | T: C-terminal domain of Npl4 | F: F_UNCLASSIFIED | ECOD (1.6) |
G | F_UNCLASSIFIED | e8datG4 | A: a+b three layers | X: Cytidine deaminase-like (From Topology) | H: Cytidine deaminase-like (From Topology) | T: Cytidine deaminase-like | F: F_UNCLASSIFIED | ECOD (1.6) |
G | F_UNCLASSIFIED | e8datG2 | A: few secondary structure elements | X: Npl4 zinc binding domain (From Topology) | H: Npl4 zinc binding domain (From Topology) | T: Npl4 zinc binding domain | F: F_UNCLASSIFIED | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF02933 | Cell division protein 48 (CDC48), domain 2 (CDC48_2) | Cell division protein 48 (CDC48), domain 2 | This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at t ... | Domain | |
PF17862 | AAA+ lid domain (AAA_lid_3) | AAA+ lid domain | This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. | Domain | |
PF00004 | ATPase family associated with various cellular activities (AAA) (AAA) | ATPase family associated with various cellular activities (AAA) | AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2]. | Domain | |
PF02359 | Cell division protein 48 (CDC48), N-terminal domain (CDC48_N) | Cell division protein 48 (CDC48), N-terminal domain | This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at t ... | Domain | |
I [auth J], J [auth K], K [auth L] | PF00240 | Ubiquitin family (ubiquitin) | Ubiquitin family | This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ... | Domain |
PF05020 | NPL4 family, putative zinc binding region (zf-NPL4) | NPL4 family, putative zinc binding region | - | Family | |
PF05021 | NPL4 family (NPL4) | NPL4 family | - | Family | |