Cryo-EM structure of NHEJ supercomplex(trimer)
Resolution: 7.76 Å
EM Method: Single-particle
Fitted PDBs: 8bot
Q-score: 0.128
Hardwick SW, Stavridi AK, Chirgadze DY, De Oliveira TM, Charbonnier JB, Ropars V, Meek K, Blundell TL, Chaplin AK
Structure (2023) 31 pp. 895- [ Pubmed: 37311458 DOI: doi:10.1016/j.str.2023.05.013 ]
- Dna (24-mer) (7 kDa, DNA from Homo sapiens)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (28-mer) (8 kDa, DNA from Homo sapiens)
- Dna (27-mer) (8 kDa, DNA from Homo sapiens)
- Dna (24-mer) (7 kDa, DNA from Homo sapiens)
- Nhej supercomplex trimer (2 MDa, Cellular component from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 7zyg
Q-score: 0.512
Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
Sci Adv (2023) 9 pp. eadg2834-eadg2834 [ Pubmed: 37256950 DOI: doi:10.1126/sciadv.adg2834 ]
- Phosphate ion (94 Da, Ligand)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Ku70/80 hetero dimer bound to dna, paxx and xlf (160 kDa, Cellular component from Homo sapiens)
- Dna (4 kDa, DNA from Homo sapiens)
- Dna (4 kDa, DNA from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
DNA-PK Ku80 mediated dimer bound to PAXX
Resolution: 4.55 Å
EM Method: Single-particle
Fitted PDBs: 8bh3
Q-score: 0.185
Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
Sci Adv (2023) 9 pp. eadg2834-eadg2834 [ Pubmed: 37256950 DOI: doi:10.1126/sciadv.adg2834 ]
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Dna (25-mer) (7 kDa, DNA from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- Nhej supercomplex bound to paxx (1 MDa, Complex from Homo sapiens)
- Dna (26-mer) (8 kDa, DNA from Homo sapiens)
- Dna (28-mer) (8 kDa, DNA from Homo sapiens)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Dna (27-mer) (8 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
DNA-PK XLF mediated dimer bound to PAXX
Resolution: 4.51 Å
EM Method: Single-particle
Fitted PDBs: 8bhv
Q-score: 0.203
Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
Sci Adv (2023) 9 pp. eadg2834-eadg2834 [ Pubmed: 37256950 DOI: doi:10.1126/sciadv.adg2834 ]
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Dna (28-mer) (7 kDa, DNA from Homo sapiens)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Dna (27-mer) (8 kDa, DNA from Homo sapiens)
- Dna-pk xlf mediated dimer bound to paxx (1 MDa, Complex from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (26-mer) (8 kDa, DNA from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- Dna (24-mer) (7 kDa, DNA from Homo sapiens)
DNA-PK Ku80 mediated dimer bound to PAXX and XLF
Resolution: 5.33 Å
EM Method: Single-particle
Fitted PDBs: 8bhy
Q-score: 0.166
Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
Sci Adv (2023) 9 pp. eadg2834-eadg2834 [ Pubmed: 37256950 DOI: doi:10.1126/sciadv.adg2834 ]
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Dna (27-mer) (8 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (25-mer) (7 kDa, DNA from Homo sapiens)
- Dna (5'-d(p*ap*ap*tp*ap*ap*tp*ap*gp*tp*tp*tp*tp*tp*ap*gp*tp*tp*tp*ap*tp*tp*gp*gp*g)-3') (7 kDa, DNA from Homo sapiens)
- Dna (26-mer) (7 kDa, DNA from Homo sapiens)
- Dna-pk ku80 mediated dimer bound to paxx and xlf (1 MDa, Cellular component from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
CryoEM structure of Ku heterodimer bound to DNA and PAXX
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7zwa
Q-score: 0.523
Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
Sci Adv (2023) 9 pp. eadg2834-eadg2834 [ Pubmed: 37256950 DOI: doi:10.1126/sciadv.adg2834 ]
- Phosphate ion (94 Da, Ligand)
- Ku70/80 heterodimer bound to dna and paxx (150 kDa, Cellular component from Homo sapiens)
- Dna (5'-d(p*gp*ap*tp*cp*cp*cp*tp*cp*tp*ap*gp*ap*tp*ap*t)-3') (4 kDa, DNA from Homo sapiens)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*gp*ap*tp*ap*tp*cp*tp*ap*gp*ap*gp*gp*gp*ap*tp*c)-3') (4 kDa, DNA from Homo sapiens)
CryoEM structure of Ku heterodimer bound to DNA
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 7zvt
Q-score: 0.554
Kefala Stavridi A, Gontier A, Morin V, Frit P, Ropars V, Barboule N, Racca C, Jonchhe S, Morten MJ, Andreani J, Rak A, Legrand P, Bourand-Plantefol A, Hardwick SW, Chirgadze DY, Davey P, De Oliveira TM, Rothenberg E, Britton S, Calsou P, Blundell TL, Varela PF, Chaplin AK, Charbonnier JB
Nucleic Acids Res (2023) 51 pp. 11732-11747 [ Pubmed: 37870477 DOI: doi:10.1093/nar/gkad863 ]
- Dna (5'-d(p*tp*cp*cp*cp*tp*cp*tp*ap*gp*ap*tp*ap*tp*c)-3') (4 kDa, DNA from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Ku70/80 heterodimer bound to dna (150 kDa, Cellular component from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*gp*ap*tp*ap*tp*cp*tp*ap*gp*ap*gp*gp*gp*ap*t)-3') (4 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7zt6
Q-score: 0.387
Kefala Stavridi A, Gontier A, Morin V, Frit P, Ropars V, Barboule N, Racca C, Jonchhe S, Morten MJ, Andreani J, Rak A, Legrand P, Bourand-Plantefol A, Hardwick SW, Chirgadze DY, Davey P, De Oliveira TM, Rothenberg E, Britton S, Calsou P, Blundell TL, Varela PF, Chaplin AK, Charbonnier JB
Nucleic Acids Res (2023) 51 pp. 11732-11747 [ Pubmed: 37870477 DOI: doi:10.1093/nar/gkad863 ]
- Cryo-em structure of ku 70/80 bound to inositol hexakisphosphate (Complex from Homo sapiens)
- X-ray repair cross-complementing protein 6 (73 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
Cryo-EM structure of NHEJ super-complex (dimer)
Resolution: 4.14 Å
EM Method: Single-particle
Fitted PDBs: 7nfc
Q-score: 0.2
Chaplin AK, Hardwick SW, Stavridi AK, Buehl CJ, Goff NJ, Ropars V, Liang S, De Oliveira TM, Chirgadze DY, Meek K, Charbonnier JB, Blundell TL
Mol Cell (2021) 81 pp. 3400-3409 [ Pubmed: 34352203 DOI: doi:10.1016/j.molcel.2021.07.005 ]
- Dna-dependent protein kinase catalytic subunit,dna-dependent protein kinase catalytic subunit,dna-pkcs (471 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (Cellular component from Homo sapiens)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- Repair protein and ligase (Cellular component from Homo sapiens)
- Nhej super-complex (dimer) (1 MDa, Cellular component)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (Cellular component from Homo sapiens)
- Dna (28-mer) (8 kDa, DNA from Homo sapiens)
- Dna (27-mer) (8 kDa, DNA from Homo sapiens)
- Dna (27-mer) (8 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing proteins 5 and 6 (Cellular component from Homo sapiens)
Cryo-EM structure of NHEJ super-complex (monomer)
Resolution: 4.29 Å
EM Method: Single-particle
Fitted PDBs: 7nfe
Q-score: 0.203
Chaplin AK, Hardwick SW, Stavridi AK, Buehl CJ, Goff NJ, Ropars V, Liang S, De Oliveira TM, Chirgadze DY, Meek K, Charbonnier JB, Blundell TL
Mol Cell (2021) 81 pp. 3400-3409 [ Pubmed: 34352203 DOI: doi:10.1016/j.molcel.2021.07.005 ]
- Dna-dependent protein kinase catalytic subunit (Cellular component from Homo sapiens)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit,dna-dependent protein kinase catalytic subunit,dna-dependent protein kinase catalytic subunit (472 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*ap*ap*tp*ap*ap*ap*cp*tp*ap*ap*ap*ap*ap*cp*tp*ap*tp*tp*ap*tp*tp*ap*tp*g)-3') (7 kDa, DNA from Homo sapiens)
- Non-homologous end-joining factor 1,dna repair protein xrcc4, dna ligase 4 (Cellular component from Homo sapiens)
- X-ray repair cross-complementing protein 6 and 5 (Cellular component from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (Cellular component from Homo sapiens)
- Nhej super-complex (monomer) (800 kDa, Cellular component)
- Dna (5'-d(p*tp*ap*ap*tp*ap*ap*tp*ap*gp*tp*tp*tp*tp*tp*ap*gp*tp*tp*tp*ap*tp*tp*ap*g)-3') (7 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)