8BOT
Cryo-EM structure of NHEJ supercomplex(trimer)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth K] | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8036636 | 3001502 | SCOP2B (2021-05-27) |
A [auth K] | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8036633 | 3001319 | SCOP2B (2021-05-27) |
B [auth L] | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8036633 | 3001319 | SCOP2B (2021-05-27) |
B [auth L] | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8036636 | 3001502 | SCOP2B (2021-05-27) |
D [auth N] | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8036636 | 3001502 | SCOP2B (2021-05-27) |
D [auth N] | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8036633 | 3001319 | SCOP2B (2021-05-27) |
E [auth O] | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8036636 | 3001502 | SCOP2B (2021-05-27) |
E [auth O] | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8036633 | 3001319 | SCOP2B (2021-05-27) |
F [auth P] | SCOP2B Superfamily | DNA ligase IV Xrcc4-binding domain-like | 8095958 | 3002713 | SCOP2B (2021-05-27) |
C [auth M] | SCOP2B Superfamily | DNA ligase IV Xrcc4-binding domain-like | 8095958 | 3002713 | SCOP2B (2021-05-27) |
G [auth Q] | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8051828 | 3001502 | SCOP2B (2021-05-27) |
G [auth Q] | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8051827 | 3001319 | SCOP2B (2021-05-27) |
H [auth R] | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8051828 | 3001502 | SCOP2B (2021-05-27) |
H [auth R] | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8051827 | 3001319 | SCOP2B (2021-05-27) |
X | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8051827 | 3001319 | SCOP2B (2021-05-27) |
X | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8051828 | 3001502 | SCOP2B (2021-05-27) |
Y | SCOP2B Superfamily | XRCC4 C-terminal oligomerization domain-like | 8051828 | 3001502 | SCOP2B (2021-05-27) |
Y | SCOP2B Superfamily | XRCC4 N-terminal domain-like | 8051827 | 3001319 | SCOP2B (2021-05-27) |
J [auth G] | SCOP2B Superfamily | vWA-like | 8035574 | 3000832 | SCOP2B (2021-05-27) |
J [auth G] | SCOP2B Superfamily | SPOC domain-like | 8035571 | 3000675 | SCOP2B (2021-05-27) |
O [auth B] | SCOP2B Superfamily | vWA-like | 8035574 | 3000832 | SCOP2B (2021-05-27) |
O [auth B] | SCOP2B Superfamily | SPOC domain-like | 8035571 | 3000675 | SCOP2B (2021-05-27) |
T | SCOP2B Superfamily | SPOC domain-like | 8035571 | 3000675 | SCOP2B (2021-05-27) |
T | SCOP2B Superfamily | vWA-like | 8035574 | 3000832 | SCOP2B (2021-05-27) |
K [auth H] | SCOP2B Superfamily | vWA-like | 8035579 | 3000832 | SCOP2B (2021-05-27) |
K [auth H] | SCOP2B Superfamily | SPOC domain-like | 8035577 | 3000675 | SCOP2B (2021-05-27) |
K [auth H] | SCOP2B Superfamily | C-terminal domain of Ku80 | 8041016 | 3001210 | SCOP2B (2021-05-27) |
P [auth C] | SCOP2B Superfamily | SPOC domain-like | 8035577 | 3000675 | SCOP2B (2021-05-27) |
P [auth C] | SCOP2B Superfamily | vWA-like | 8035579 | 3000832 | SCOP2B (2021-05-27) |
U | SCOP2B Superfamily | C-terminal domain of Ku80 | 8041016 | 3001210 | SCOP2B (2021-05-27) |
U | SCOP2B Superfamily | SPOC domain-like | 8035577 | 3000675 | SCOP2B (2021-05-27) |
U | SCOP2B Superfamily | vWA-like | 8035579 | 3000832 | SCOP2B (2021-05-27) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth K] | PF06632 | e8botK2 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF06632 | ECOD (1.6) |
A [auth K] | F_UNCLASSIFIED | e8botK3 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
A [auth K] | PF21924 | e8botK1 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21924 | ECOD (1.6) |
B [auth L] | PF06632 | e8botL2 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF06632 | ECOD (1.6) |
B [auth L] | F_UNCLASSIFIED | e8botL1 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
B [auth L] | PF21924 | e8botL3 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21924 | ECOD (1.6) |
D [auth N] | PF06632 | e8botN3 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF06632 | ECOD (1.6) |
D [auth N] | F_UNCLASSIFIED | e8botN1 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
D [auth N] | PF21924 | e8botN2 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21924 | ECOD (1.6) |
E [auth O] | PF06632 | e8botO3 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF06632 | ECOD (1.6) |
E [auth O] | F_UNCLASSIFIED | e8botO2 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
E [auth O] | PF21924 | e8botO1 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21924 | ECOD (1.6) |
G [auth Q] | PF09302 | e8botQ1 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF09302 | ECOD (1.6) |
G [auth Q] | F_UNCLASSIFIED | e8botQ2 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
G [auth Q] | PF21928 | e8botQ3 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21928 | ECOD (1.6) |
H [auth R] | PF09302 | e8botR2 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF09302 | ECOD (1.6) |
H [auth R] | F_UNCLASSIFIED | e8botR3 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
H [auth R] | PF21928 | e8botR1 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21928 | ECOD (1.6) |
X | PF09302 | e8botX2 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF09302 | ECOD (1.6) |
X | F_UNCLASSIFIED | e8botX1 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
X | PF21928 | e8botX3 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21928 | ECOD (1.6) |
Y | PF09302 | e8botY3 | A: beta barrels | X: XRCC4, N-terminal domain-like | H: XRCC4, N-terminal domain (From Topology) | T: XRCC4, N-terminal domain | F: PF09302 | ECOD (1.6) |
Y | F_UNCLASSIFIED | e8botY2 | A: alpha arrays | X: HTH | H: HTH | T: HTH motif inserted in other structures | F: F_UNCLASSIFIED | ECOD (1.6) |
Y | PF21928 | e8botY1 | A: alpha duplicates or obligate multimers | X: XRCC4 C-terminal oligomerization domain (From Topology) | H: XRCC4 C-terminal oligomerization domain (From Topology) | T: XRCC4 C-terminal oligomerization domain | F: PF21928 | ECOD (1.6) |
J [auth G] | PF02735,PF03730 | e8botG2 | A: beta barrels | X: SPOC domain-like | H: SPOC domain-related | T: Ku70/80 subunit middle domain | F: PF02735,PF03730 | ECOD (1.6) |
J [auth G] | PF03731 | e8botG1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03731 | ECOD (1.6) |
O [auth B] | PF02735,PF03730 | e8botB2 | A: beta barrels | X: SPOC domain-like | H: SPOC domain-related | T: Ku70/80 subunit middle domain | F: PF02735,PF03730 | ECOD (1.6) |
O [auth B] | PF03731 | e8botB1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03731 | ECOD (1.6) |
T | PF02735,PF03730 | e8botT2 | A: beta barrels | X: SPOC domain-like | H: SPOC domain-related | T: Ku70/80 subunit middle domain | F: PF02735,PF03730 | ECOD (1.6) |
T | PF03731 | e8botT1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03731 | ECOD (1.6) |
K [auth H] | PF02735,PF03730 | e8botH1 | A: beta barrels | X: SPOC domain-like | H: SPOC domain-related | T: Ku70/80 subunit middle domain | F: PF02735,PF03730 | ECOD (1.6) |
K [auth H] | PF08785 | e8botH3 | A: alpha superhelices | X: Repetitive alpha hairpins | H: C-terminal domain of Ku80 (From Topology) | T: C-terminal domain of Ku80 | F: PF08785 | ECOD (1.6) |
K [auth H] | PF03731 | e8botH2 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03731 | ECOD (1.6) |
P [auth C] | PF02735,PF03730 | e8botC2 | A: beta barrels | X: SPOC domain-like | H: SPOC domain-related | T: Ku70/80 subunit middle domain | F: PF02735,PF03730 | ECOD (1.6) |
P [auth C] | PF03731 | e8botC1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03731 | ECOD (1.6) |
U | PF02735,PF03730 | e8botU1 | A: beta barrels | X: SPOC domain-like | H: SPOC domain-related | T: Ku70/80 subunit middle domain | F: PF02735,PF03730 | ECOD (1.6) |
U | PF08785 | e8botU3 | A: alpha superhelices | X: Repetitive alpha hairpins | H: C-terminal domain of Ku80 (From Topology) | T: C-terminal domain of Ku80 | F: PF08785 | ECOD (1.6) |
U | PF03731 | e8botU2 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03731 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth K], B [auth L], D [auth N], E [auth O] | PF06632 | XRCC4 N-terminal domain (XRCC4) | XRCC4 N-terminal domain | This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRC ... | Domain |
A [auth K], B [auth L], D [auth N], E [auth O] | PF21924 | XRCC4 coiled-coil (XRCC4_CC) | XRCC4 coiled-coil | - | Coiled-coil |
C [auth M], F [auth P] | PF11411 | DNA ligase IV (DNA_ligase_IV) | DNA ligase IV | - | Family |
C [auth M], F [auth P] | PF00533 | BRCA1 C Terminus (BRCT) domain (BRCT) | BRCA1 C Terminus (BRCT) domain | - | Family |
G [auth Q], H [auth R], X, Y | PF09302 | XLF N-terminal domain (XLF) | XLF N-terminal domain | XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human ... | Domain |
G [auth Q], H [auth R], X, Y | PF21928 | XLF protein coiled-coil region (XLF_CC) | XLF protein coiled-coil region | - | Coiled-coil |
I [auth F], N [auth A], S | PF08163 | DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3) | DNA-dependent protein kinase catalytic subunit, CC3 | - | Repeat |
I [auth F], N [auth A], S | PF02260 | FATC domain (FATC) | FATC domain | - | Family |
I [auth F], N [auth A], S | PF00454 | Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase) | Phosphatidylinositol 3- and 4-kinase | - | Family |
I [auth F], N [auth A], S | PF20502 | DNA-dependent protein kinase catalytic subunit, CC1/2 (DNAPKcs_CC1-2) | DNA-dependent protein kinase catalytic subunit, CC1/2 | - | Repeat |
I [auth F], N [auth A], S | PF02259 | FAT domain (FAT) | FAT domain | - | Repeat |
I [auth F], N [auth A], S | PF19704 | DNA-PKcs, CC5 (DNAPKcs_CC5) | DNA-PKcs, CC5 | - | Repeat |
J [auth G], O [auth B], T | PF02735 | Ku70/Ku80 beta-barrel domain (Ku) | Ku70/Ku80 beta-barrel domain | The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ... | Domain |
J [auth G], O [auth B], T | PF03730 | Ku70/Ku80 C-terminal arm (Ku_C) | Ku70/Ku80 C-terminal arm | - | Family |
J [auth G], O [auth B], T | PF03731 | Ku70/Ku80 N-terminal alpha/beta domain (Ku_N) | Ku70/Ku80 N-terminal alpha/beta domain | The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ... | Domain |
K [auth H], P [auth C], U | PF02735 | Ku70/Ku80 beta-barrel domain (Ku) | Ku70/Ku80 beta-barrel domain | The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ... | Domain |
K [auth H], P [auth C], U | PF08785 | Ku C terminal domain like (Ku_PK_bind) | Ku C terminal domain like | The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DN ... | Domain |
K [auth H], P [auth C], U | PF03730 | Ku70/Ku80 C-terminal arm (Ku_C) | Ku70/Ku80 C-terminal arm | - | Family |
K [auth H], P [auth C], U | PF03731 | Ku70/Ku80 N-terminal alpha/beta domain (Ku_N) | Ku70/Ku80 N-terminal alpha/beta domain | The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ... | Domain |