Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in 90PS with beryllium fluoride (E2P state)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7drx
Q-score: 0.556
Cell Rep (2022) 38 pp. 110518-110518 [ Pubmed: 35294892 DOI: doi:10.1016/j.celrep.2022.110518 ]
- Dnf1_lem3 complex (Complex from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- (4s,7r)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
- Alkylphosphocholine resistance protein lem3 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phospholipid-transporting atpase dnf1 (178 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in 90PS with AMPPCP (E1-ATP state)
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 7dsh
Q-score: 0.428
Cell Rep (2022) 38 pp. 110518-110518 [ Pubmed: 35294892 DOI: doi:10.1016/j.celrep.2022.110518 ]
- Dnf1_lem3 complex (Complex from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Alkylphosphocholine resistance protein lem3 (47 kDa, Protein from Saccharomyces cerevisiae)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Phospholipid-transporting atpase dnf1 (178 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 7dsi
Q-score: 0.422
Cell Rep (2022) 38 pp. 110518-110518 [ Pubmed: 35294892 DOI: doi:10.1016/j.celrep.2022.110518 ]
- Dnf1_lem3 complex (Complex from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Alkylphosphocholine resistance protein lem3 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phospholipid-transporting atpase dnf1 (178 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.81 Å
EM Method: Single-particle
Fitted PDBs: 7f7f
Q-score: 0.379
Cell Rep (2022) 38 pp. 110518-110518 [ Pubmed: 35294892 DOI: doi:10.1016/j.celrep.2022.110518 ]
- Magnesium ion (24 Da, Ligand)
- Alkylphosphocholine resistance protein lem3 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phospholipid-transporting atpase dnf1 (178 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dnf1_lem3 complex (Complex from Saccharomyces cerevisiae S288C)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7whv
Q-score: 0.573
Cell Rep (2022) 38 pp. 110518-110518 [ Pubmed: 35294892 DOI: doi:10.1016/j.celrep.2022.110518 ]
- Dnf1_lem3 complex (Complex from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- (4s,7r)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
- Alkylphosphocholine resistance protein lem3 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phospholipid-transporting atpase dnf1 (178 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in detergent with AMPPCP (E1-ATP state)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7whw
Q-score: 0.437
Cell Rep (2022) 38 pp. 110518-110518 [ Pubmed: 35294892 DOI: doi:10.1016/j.celrep.2022.110518 ]
- Dnf1_lem3 complex (Complex from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Alkylphosphocholine resistance protein lem3 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phospholipid-transporting atpase dnf1 (178 kDa, Protein from Saccharomyces cerevisiae S288C)
Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6h67
Q-score: 0.409
Sanz-Murillo M, Xu J, Belogurov GA, Calvo O, Gil-Carton D, Moreno-Morcillo M, Wang D, Fernandez-Tornero C
PNAS (2018) 115 pp. 8972-8977 [ DOI: doi:10.1073/pnas.1802626115 Pubmed: 30127008 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase i stalling at dna damage (631 kDa, Complex)
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (15 kDa, DNA from Saccharomyces cerevisiae)
- Rna polymerase i stalling at dna damage (Complex from Saccharomyces cerevisiae)
- Rna polymerase i stalling at dna damage (Complex from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Non-template dna (16 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6h68
Q-score: 0.247
Sanz-Murillo M, Xu J, Belogurov GA, Calvo O, Gil-Carton D, Moreno-Morcillo M, Wang D, Fernandez-Tornero C
PNAS (2018) 115 pp. 8972-8977 [ DOI: doi:10.1073/pnas.1802626115 Pubmed: 30127008 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase i stalling at dna damage (631 kDa, Complex)
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (15 kDa, DNA from Saccharomyces cerevisiae)
- Rna polymerase i stalling at dna damage (Complex from Saccharomyces cerevisiae)
- Rna polymerase i stalling at dna damage (Complex from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Non-template dna (16 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Ternary complex of RNA Pol II, transcription scaffold and Rad26
Resolution: 5.8 Å
EM Method: Single-particle
Fitted PDBs: 5vvr
Q-score: 0.174
Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D
Nature (2017) 551 pp. 653-657 [ DOI: doi:10.1038/nature24658 Pubmed: 29168508 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (nts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Dna (ts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Ternary complex of rna pol ii, transcription scaffold and rad26 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair and recombination protein rad26 (124 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 6.4 Å
EM Method: Single-particle
Fitted PDBs: 5vvs
Q-score: 0.184
Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D
Nature (2017) 551 pp. 653-657 [ DOI: doi:10.1038/nature24658 Pubmed: 29168508 ]
- Binary complex of rna pol ii and transcription scaffold (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (nts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (ts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))