Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network
Lee RG, Rudler DL, Raven SA, Peng L, Chopin A, Moh ESX, McCubbin T, Siira SJ, Fagan SV, DeBono NJ, Stentenbach M, Browne J, Rackham FF, Li J, Simpson KJ, Marcellin E, Packer NH, Reid GE, Padman BS, Rackham O, Filipovska A
Nature cell Biology ()
Image sets:
- Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 wt cells (Sample A)
- Unprocessed FIB-SEM slices acquired from Cal51 PEX26ko cells (Sample B)
- AIVE outputs generated from FIB-SEM data of Cal51 GOLGA5ko cells (Sample C)
- Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC61A2ko cells (Sample E)
- AIVE outputs generated from FIB-SEM data of Cal51 SEC61A2ko cells (Sample E)
- Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC62ko cells (Sample F)
- AIVE outputs generated from FIB-SEM data of Cal51 SEC62ko cells (Sample F)
- Unprocessed FIB-SEM slices acquired from Cal51 GOLGA5ko cells (Sample C)
- AIVE outputs generated from FIB-SEM data of Cal51 wt cells (Sample A).
- Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA8Mko cells (Sample D)
- AIVE outputs generated from FIB-SEM data of Cal51 PEX26ko cells (Sample B)
- Unprocessed FIB-SEM slices acquired from Cal51 GOLGA8Mko cells (Sample D)
- AIVE outputs generated from FIB-SEM data of Cal51 GOLGA8Mko cells (Sample D)
- Unprocessed FIB-SEM slices acquired from Cal51 SEC62ko cells (Sample F)
- Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 PEX26ko cells (Sample B)
- Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA5ko cells (Sample C)
- Unprocessed FIB-SEM slices acquired from Cal51 wt cells (Sample A)
- Unprocessed FIB-SEM slices acquired from Cal51 SEC61A2ko cells (Sample E)
DNA-PK complex of DNA end processing
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7sgl
Q-score: 0.445
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177- [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein artemis (79 kDa, Protein from Homo sapiens)
- Complex of dna-pkcs, ku70, ku80, artemis and dna (720 kDa, Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- X-ray repair cross-complementing protein 6 (70 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Hairpin_1 (16 kDa, DNA from synthetic construct)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
FATKIN domain of the phosphorylated DNA-PKcs
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177-189.e4 [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Ku80 (Protein from Homo sapiens)
- Dna-pkcs/ku/artemis/dna complex (720 kDa, Complex)
- Hairpin_1 (DNA from synthetic construct)
- Ku70 (Protein from Homo sapiens)
- Protein artemis (Protein from Homo sapiens)
- Dna-pkcs (Protein from Homo sapiens)
KU, Artemis, DNA and DNA-PKcs_Nheat in the NHEJ DNA end processing complex
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177-189.e4 [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Ku80 (Protein from Homo sapiens)
- Artemis (Protein from Homo sapiens)
- Hairpin_1 (DNA from synthetic construct)
- Ku70 (Protein from Homo sapiens)
- Complex of dna-pkcs, ku70, ku80, artemis and dna (720 kDa, Complex)
- Dna-pkcs (Protein from Homo sapiens)
CryoEM structure of DNA-PK complex VII
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7su3
Q-score: 0.528
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177- [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Dna (5'-d(*gp*cp*ap*tp*gp*cp*tp*cp*tp*ap*cp*tp*gp*cp*tp*tp*cp*gp*ap*tp*ap*tp*cp*g)-3') (7 kDa, DNA from Escherichia coli)
- Dna (5'-d(*ap*ap*gp*cp*ap*gp*tp*ap*gp*ap*g)-3') (4 kDa, DNA from Escherichia coli)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna-pk complex vii (Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
CryoEM structure of DNA-PK complex VIII
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7sud
Q-score: 0.403
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177- [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Dna-pk (Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)