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Cryo-EM structure of NHEJ supercomplex(trimer)

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth K]SCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8036636 3001502 SCOP2B (2022-06-29)
A [auth K]SCOP2B SuperfamilyXRCC4 N-terminal domain-like 8036633 3001319 SCOP2B (2022-06-29)
E [auth O]SCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8036636 3001502 SCOP2B (2022-06-29)
E [auth O]SCOP2B SuperfamilyXRCC4 N-terminal domain-like 8036633 3001319 SCOP2B (2022-06-29)
D [auth N]SCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8036636 3001502 SCOP2B (2022-06-29)
D [auth N]SCOP2B SuperfamilyXRCC4 N-terminal domain-like 8036633 3001319 SCOP2B (2022-06-29)
B [auth L]SCOP2B SuperfamilyXRCC4 N-terminal domain-like 8036633 3001319 SCOP2B (2022-06-29)
B [auth L]SCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8036636 3001502 SCOP2B (2022-06-29)
F [auth P]SCOP2B SuperfamilyDNA ligase IV Xrcc4-binding domain-like 8095958 3002713 SCOP2B (2022-06-29)
C [auth M]SCOP2B SuperfamilyDNA ligase IV Xrcc4-binding domain-like 8095958 3002713 SCOP2B (2022-06-29)
G [auth Q]SCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8051828 3001502 SCOP2B (2022-06-29)
G [auth Q]SCOP2B SuperfamilyXRCC4 N-terminal domain-like 8051827 3001319 SCOP2B (2022-06-29)
H [auth R]SCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8051828 3001502 SCOP2B (2022-06-29)
H [auth R]SCOP2B SuperfamilyXRCC4 N-terminal domain-like 8051827 3001319 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyXRCC4 N-terminal domain-like 8051827 3001319 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8051828 3001502 SCOP2B (2022-06-29)
YSCOP2B SuperfamilyXRCC4 C-terminal oligomerization domain-like 8051828 3001502 SCOP2B (2022-06-29)
YSCOP2B SuperfamilyXRCC4 N-terminal domain-like 8051827 3001319 SCOP2B (2022-06-29)
J [auth G]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
J [auth G]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
TSCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
TSCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
O [auth B]SCOP2B SuperfamilyvWA-like 8035574 3000832 SCOP2B (2022-06-29)
O [auth B]SCOP2B SuperfamilySPOC domain-like 8035571 3000675 SCOP2B (2022-06-29)
K [auth H]SCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)
K [auth H]SCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
K [auth H]SCOP2B SuperfamilyC-terminal domain of Ku80 8041016 3001210 SCOP2B (2022-06-29)
P [auth C]SCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
P [auth C]SCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)
USCOP2B SuperfamilyC-terminal domain of Ku80 8041016 3001210 SCOP2B (2022-06-29)
USCOP2B SuperfamilySPOC domain-like 8035577 3000675 SCOP2B (2022-06-29)
USCOP2B SuperfamilyvWA-like 8035579 3000832 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth K],
B [auth L],
D [auth N],
E [auth O]		PF06632XRCC4 N-terminal domain (XRCC4)XRCC4 N-terminal domainThis 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 ...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 XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks [1]. This entry represents the N-terminal beta sandwich domain.
Domain
A [auth K],
B [auth L],
D [auth N],
E [auth O]		PF21924XRCC4 coiled-coil (XRCC4_CC)XRCC4 coiled-coil- Coiled-coil
C [auth M],
F [auth P]		PF11411DNA ligase IV (DNA_ligase_IV)DNA ligase IV- Family
C [auth M],
F [auth P]		PF00533BRCA1 C Terminus (BRCT) domain (BRCT)BRCA1 C Terminus (BRCT) domainThe BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- ...The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5].
Domain
G [auth Q],
H [auth R],
X,
Y		PF09302XLF N-terminal domain (XLF)XLF N-terminal domainXLF (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 ...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 cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining [1]. This family contains Nej1 (non-homologous end-joining factor) [2], and Lif1, ligase-interacting factor [3]. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining [4]. This entry represents the N-terminal beta sandwich domain of XLF.
Domain
G [auth Q],
H [auth R],
X,
Y		PF21928XLF protein coiled-coil region (XLF_CC)XLF protein coiled-coil region- Coiled-coil
J [auth G],
O [auth B],
T		PF02735Ku70/Ku80 beta-barrel domain (Ku)Ku70/Ku80 beta-barrel domainThe 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 ...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-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].
Domain
J [auth G],
O [auth B],
T		PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
J [auth G],
O [auth B],
T		PF03731Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)Ku70/Ku80 N-terminal alpha/beta domainThe 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 ...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 alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].
Domain
K [auth H],
P [auth C],
U		PF02735Ku70/Ku80 beta-barrel domain (Ku)Ku70/Ku80 beta-barrel domainThe 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 ...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-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].
Domain
K [auth H],
P [auth C],
U		PF08785Ku C terminal domain like (Ku_PK_bind)Ku C terminal domain likeThe 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 DNA ...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 DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs [1].
Domain
K [auth H],
P [auth C],
U		PF03730Ku70/Ku80 C-terminal arm (Ku_C)Ku70/Ku80 C-terminal arm- Family
K [auth H],
P [auth C],
U		PF03731Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)Ku70/Ku80 N-terminal alpha/beta domainThe 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 ...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 alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].
Domain
I [auth F],
N [auth A],
S		PF08163DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3)DNA-dependent protein kinase catalytic subunit, CC3- Repeat
I [auth F],
N [auth A],
S		PF02260FATC domain (FATC)FATC domain- Family
I [auth F],
N [auth A],
S		PF00454Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)Phosphatidylinositol 3- and 4-kinase- Family
I [auth F],
N [auth A],
S		PF02259FAT domain (FAT)FAT domain- Repeat
I [auth F],
N [auth A],
S		PF19704DNA-PKcs, CC5 (DNAPKcs_CC5)DNA-PKcs, CC5- Repeat
I [auth F],
N [auth A],
S		PF20502DNA-dependent protein kinase catalytic subunit, CC1/2 (DNAPKcs_CC1-2)DNA-dependent protein kinase catalytic subunit, CC1/2- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth K],
B [auth L],
D [auth N],
E [auth O]		DNA repair protein XRCC4
C [auth M],
F [auth P]		DNA ligase 4
G [auth Q],
H [auth R],
X,
Y		Non-homologous end-joining factor 1
J [auth G],
O [auth B],
T		X-ray repair cross-complementing protein 6
K [auth H],
P [auth C],
U		X-ray repair cross-complementing protein 5
L [auth I],
V		DNA (28-MER)---
M [auth J],
W		DNA (27-MER)---
Q [auth D]DNA (24-MER)---
R [auth E]DNA (24-MER)---
I [auth F],
N [auth A],
S		DNA-dependent protein kinase catalytic subunit

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR053963XRCC4, C-terminal domainDomain
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR038051XRCC4-like, N-terminal domain superfamilyHomologous Superfamily
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR009089XRCC4, N-terminal domain superfamilyHomologous Superfamily
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR014751DNA repair protein XRCC4-like, C-terminalHomologous Superfamily
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR053961XRCC4, N-terminal domainDomain
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR010585DNA repair protein XRCC4Family
A [auth K],
B [auth L],
D [auth N],
E [auth O]		IPR053962XRCC4, coiled-coil domainDomain
C [auth M],
F [auth P]		IPR029710DNA ligase 4Family
C [auth M],
F [auth P]		IPR012310DNA ligase, ATP-dependent, centralDomain
C [auth M],
F [auth P]		IPR012308DNA ligase, ATP-dependent, N-terminalDomain
C [auth M],
F [auth P]		IPR044125DNA Ligase 4, adenylation domainDomain
C [auth M],
F [auth P]		IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
C [auth M],
F [auth P]		IPR021536DNA ligase IV domainDomain
C [auth M],
F [auth P]		IPR036599DNA ligase, ATP-dependent, N-terminal domain superfamilyHomologous Superfamily
C [auth M],
F [auth P]		IPR001357BRCT domainDomain
C [auth M],
F [auth P]		IPR036420BRCT domain superfamilyHomologous Superfamily
C [auth M],
F [auth P]		IPR016059DNA ligase, ATP-dependent, conserved siteConserved Site
C [auth M],
F [auth P]		IPR000977DNA ligase, ATP-dependentFamily
C [auth M],
F [auth P]		IPR012309DNA ligase, ATP-dependent, C-terminalDomain
G [auth Q],
H [auth R],
X,
Y		IPR052287Non-homologous end-joining factorFamily
G [auth Q],
H [auth R],
X,
Y		IPR015381XLF-like, N-terminalDomain
G [auth Q],
H [auth R],
X,
Y		IPR038051XRCC4-like, N-terminal domain superfamilyHomologous Superfamily
G [auth Q],
H [auth R],
X,
Y		IPR053829XLF-like, coiled-coil regionDomain
J [auth G],
O [auth B],
T		IPR016194SPOC-like, C-terminal domain superfamilyHomologous Superfamily
J [auth G],
O [auth B],
T		IPR027388Ku70, bridge and pillars domain superfamilyHomologous Superfamily
J [auth G],
O [auth B],
T		IPR036361SAP domain superfamilyHomologous Superfamily
J [auth G],
O [auth B],
T		IPR006165Ku70Family
J [auth G],
O [auth B],
T		IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
J [auth G],
O [auth B],
T		IPR005161Ku70/Ku80, N-terminal alpha/betaDomain
J [auth G],
O [auth B],
T		IPR006164Ku70/Ku80, DNA-binding domainDomain
J [auth G],
O [auth B],
T		IPR047087Ku70, core domainDomain
J [auth G],
O [auth B],
T		IPR005160Ku70/Ku80 C-terminal armDomain
J [auth G],
O [auth B],
T		IPR003034SAP domainDomain
K [auth H],
P [auth C],
U		IPR036494Ku, C-terminal domain superfamilyHomologous Superfamily
K [auth H],
P [auth C],
U		IPR016194SPOC-like, C-terminal domain superfamilyHomologous Superfamily
K [auth H],
P [auth C],
U		IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
K [auth H],
P [auth C],
U		IPR002035von Willebrand factor, type ADomain
K [auth H],
P [auth C],
U		IPR005161Ku70/Ku80, N-terminal alpha/betaDomain
K [auth H],
P [auth C],
U		IPR014893Ku, C-terminalDomain
K [auth H],
P [auth C],
U		IPR006164Ku70/Ku80, DNA-binding domainDomain
K [auth H],
P [auth C],
U		IPR005160Ku70/Ku80 C-terminal armDomain
K [auth H],
P [auth C],
U		IPR024193Ku80Family
I [auth F],
N [auth A],
S		IPR016024Armadillo-type foldHomologous Superfamily
I [auth F],
N [auth A],
S		IPR003151PIK-related kinase, FATDomain
I [auth F],
N [auth A],
S		IPR046803DNA-dependent protein kinase catalytic subunit, CC1/2Domain
I [auth F],
N [auth A],
S		IPR046804DNA-PKcs, N-terminalDomain
I [auth F],
N [auth A],
S		IPR045581DNA-dependent protein kinase catalytic subunit, CC5Domain
I [auth F],
N [auth A],
S		IPR003152FATC domainDomain
I [auth F],
N [auth A],
S		IPR012582DNA-dependent protein kinase catalytic subunit, CC3Domain
I [auth F],
N [auth A],
S		IPR011989Armadillo-like helicalHomologous Superfamily
I [auth F],
N [auth A],
S		IPR000403Phosphatidylinositol 3-/4-kinase, catalytic domainDomain
I [auth F],
N [auth A],
S		IPR050517DNA Damage Response and Repair KinaseFamily
I [auth F],
N [auth A],
S		IPR018936Phosphatidylinositol 3-/4-kinase, conserved siteConserved Site
I [auth F],
N [auth A],
S		IPR036940Phosphatidylinositol 3-/4-kinase, catalytic domain superfamilyHomologous Superfamily
I [auth F],
N [auth A],
S		IPR011009Protein kinase-like domain superfamilyHomologous Superfamily
I [auth F],
N [auth A],
S		IPR037706DNA-dependent protein kinase catalytic subunit, catalytic domainDomain
I [auth F],
N [auth A],
S		IPR014009PIK-related kinase, FAT domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth K],
B [auth L],
D [auth N],
E [auth O]		Pharos:  Q13426
C [auth M],
F [auth P]		Pharos:  P49917
G [auth Q],
H [auth R],
X,
Y		Pharos:  Q9H9Q4
J [auth G],
O [auth B],
T		Pharos:  P12956
K [auth H],
P [auth C],
U		Pharos:  P13010
I [auth F],
N [auth A],
S		Pharos:  P78527