Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS
Liang S, Liu A, Liu Y, Wang F, Zhou Y, Long Y, Wang T, Liu Z, Ren R, Ye RD
PNAS (2024) 121 pp. e2320388121-e2320388121 [ DOI: doi:10.1073/pnas.2320388121 Pubmed: 38805284 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cytochrome b-245 light chain (14 kDa, Protein from Homo sapiens)
- Monoclonal antibody 7g5 light chain (23 kDa, Protein from Oryctolagus cuniculus)
- Nadph oxidase 2 in complex with cytochrome b-245 light chain, cytochrome b-245 chaperone 1 and a monoclonal antibody (Complex from Homo sapiens)
- Cytochrome b-245 heavy chain (64 kDa, Protein from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Monoclonal antibody 7g5 heavy chain (23 kDa, Protein from Oryctolagus cuniculus)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cytochrome b-245 chaperone 1 (18 kDa, Protein from Homo sapiens)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 7z87
Q-score: 0.426
Nat Struct Mol Biol (2023) 30 pp. 140-147 [ Pubmed: 36604499 DOI: doi:10.1038/s41594-022-00881-w ]
- Human dna-dependent protein kinase (Complex from Homo sapiens)
- (~{s})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol (481 Da, Ligand)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (26-mer) (8 kDa, DNA from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Dna (26-mer) (7 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
DNA-PK in the intermediate state
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7z88
Q-score: 0.389
Nat Struct Mol Biol (2023) 30 pp. 140-147 [ Pubmed: 36604499 DOI: doi:10.1038/s41594-022-00881-w ]
- Human dna-dependent protein kinase (Complex from Homo sapiens)
- (~{s})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol (481 Da, Ligand)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna (26-mer) (8 kDa, DNA from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Dna (26-mer) (7 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
DNA-PK in complex with ATPgammaS
Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL
Nature (2022) 601 pp. 643-648 [ Pubmed: 34987222 DOI: doi:10.1038/s41586-021-04274-9 ]
Cryo-EM structure of DNA-PKcs in complex with NU7441
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7otm
Q-score: 0.394
Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL
Nature (2022) 601 pp. 643-648 [ Pubmed: 34987222 DOI: doi:10.1038/s41586-021-04274-9 ]
DNA-PKcs in complex with ATPgammaS-Mg
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7otp
Q-score: 0.414
Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL
Nature (2022) 601 pp. 643-648 [ Pubmed: 34987222 DOI: doi:10.1038/s41586-021-04274-9 ]
- Dna-pkcs in complex with nu7441 (Complex from Homo sapiens)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna-dependent protein kinase catalytic subunit,dna-pkcs (471 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
DNA-PKcs in complex with wortmannin
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 7otv
Q-score: 0.308
Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL
Nature (2022) 601 pp. 643-648 [ Pubmed: 34987222 DOI: doi:10.1038/s41586-021-04274-9 ]
- Dna-dependent protein kinase catalytic subunit,dna-dependent protein kinase catalytic subunit,dna-pkcs (471 kDa, Protein from Homo sapiens)
- Dna-pkcs in complex with wortmannin (Complex from Homo sapiens)
- (1s,6br,9as,11r,11br)-9a,11b-dimethyl-1-[(methyloxy)methyl]-3,6,9-trioxo-1,6,6b,7,8,9,9a,10,11,11b-decahydro-3h-furo[4, 3,2-de]indeno[4,5-h][2]benzopyran-11-yl acetate (428 Da, Ligand)
DNA-PKcs in complex with AZD7648
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 7otw
Q-score: 0.386
Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL
Nature (2022) 601 pp. 643-648 [ Pubmed: 34987222 DOI: doi:10.1038/s41586-021-04274-9 ]
DNA-PKcs in complex with M3814
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 7oty
Q-score: 0.462
Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL
Nature (2022) 601 pp. 643-648 [ Pubmed: 34987222 DOI: doi:10.1038/s41586-021-04274-9 ]
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 [ DOI: doi:10.1016/j.molcel.2021.07.005 Pubmed: 34352203 ]
- Repair protein and ligase (Cellular component 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 6 (69 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-pkcs (471 kDa, Protein from Homo sapiens)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Nhej super-complex (dimer) (1 MDa, Cellular component)
- X-ray repair cross-complementing proteins 5 and 6 (Cellular component 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 (Cellular component from Homo sapiens)