The cryo-EM structure of the Nicotiana tabacum PEP-PAP-TEC2
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8wa1
Q-score: 0.414
Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y
Cell (2024) 187 pp. 1127-1144.e21 [ Pubmed: 38428393 DOI: doi:10.1016/j.cell.2024.01.026 ]
- Pentatricopeptide repeat-containing protein at1g74850, chloroplastic-like (96 kDa, Protein from Nicotiana tabacum)
- Nicotiana tabacum pep-pap-tec2 (Complex from Nicotiana tabacum)
- Protein plastid transcriptionally active 12-like (61 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 7-like isoform x1 (19 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Superoxide dismutase (30 kDa, Protein from Nicotiana tabacum)
- Thioredoxin-like protein citrx1, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Pap13(ptac18) (17 kDa, Protein from Nicotiana tabacum)
- Udp-n-acetylmuramoyl-l-alanyl-d-glutamate--2, 6-diaminopimelate ligase-like (85 kDa, Protein from Nicotiana tabacum)
- Pap8(ptac6) (38 kDa, Protein from Nicotiana tabacum)
- Protein plastid transcriptionally active 10-like (80 kDa, Protein from Nicotiana tabacum)
- Dna (24-mer) (7 kDa, DNA from synthetic construct)
- Dna (24-mer) (7 kDa, DNA from synthetic construct)
- Fructokinase-like 1, chloroplastic (55 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit beta (120 kDa, Protein from Nicotiana tabacum)
- Rna (27-mer) (8 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit gamma (79 kDa, Protein from Nicotiana tabacum)
- Superoxide dismutase (34 kDa, Protein from Nicotiana tabacum)
- Fructokinase-like 2, chloroplastic (72 kDa, Protein from Nicotiana tabacum)
- Pap1(ptac3) (101 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- Protein plastid transcriptionally active 14-like isoform x2 (58 kDa, Protein from Nicotiana tabacum)
- Fe (iii) ion (55 Da, Ligand)
- Dna-directed rna polymerase subunit beta'' (157 kDa, Protein from Nicotiana tabacum)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Nicotiana tabacum)
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)
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)
CasX ternary complex with 30bp target DNA
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6ny3
Q-score: 0.465
Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA
Nature (2019) 566 pp. 218-223 [ DOI: doi:10.1038/s41586-019-0908-x Pubmed: 30718774 ]
- Casx ternary complex with 30bp target dna (Complex from Deltaproteobacteria)
- Casx (113 kDa, Protein from Deltaproteobacteria bacterium)
- Rna (122-mer) (39 kDa, RNA from Deltaproteobacteria bacterium)
- Dna (24-mer) (7 kDa, DNA from Deltaproteobacteria bacterium)
- Dna (30-mer) (9 kDa, DNA from Deltaproteobacteria bacterium)