cryoEM structure of the central Ald4 filament determined by FilamentID
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8rwk
Q-score: 0.422
Hugener J, Xu J, Wettstein R, Ioannidi L, Velikov D, Wollweber F, Henggeler A, Matos J, Pilhofer M
Cell (2024) 187 pp. 3303- [ Pubmed: 38906101 DOI: doi:10.1016/j.cell.2024.04.026 ]
OEA bound GPR3-Gs complex structure
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8x2k
Q-score: 0.532
Chen G, Staffen N, Wu Z, Xu X, Pan J, Inoue A, Shi T, Gmeiner P, Du Y, Xu J
Cell Res (2024) 34 pp. 262-265 [ Pubmed: 38287118 DOI: doi:10.1038/s41422-023-00919-8 ]
- Scfv16 (Complex)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Isoform gnas-2 of guanine nucleotide-binding protein g(s) subunit alpha isoforms short (43 kDa, Protein from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Gpr3 (Complex from Homo sapiens)
- Soluble cytochrome b562,g-protein coupled receptor 3 (50 kDa, Protein from Homo sapiens)
- (z)-n-(2-hydroxyethyl)octadec-9-enamide (325 Da, Ligand)
- Gpr3, guanine nucleotide-binding protein g(s) subunit alpha, guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1,guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Homo sapiens)
- Gpr3-gs-scfv16 complex (150 kDa, Complex from Homo sapiens)
The cryo-EM structure of E. coli CueR transcription activation complex
Resolution: 3.69 Å
EM Method: Single-particle
Fitted PDBs: 6ldi
Q-score: 0.471
Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O'Halloran TV, Zhang Y
Nat Chem Biol (2021) 17 pp. 57-64 [ DOI: doi:10.1038/s41589-020-00653-x Pubmed: 32989300 ]
- Rna (5'-r(*cp*up*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli cuer transcription activation complex (507 kDa, Complex from Escherichia coli K-12)
- Dna (50-mer) (15 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Silver ion (107 Da, Ligand)
- Dna (50-mer) (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Hth-type transcriptional regulator cuer (15 kDa, Protein from Escherichia coli (strain K12))
Resolution: 4.22 Å
EM Method: Single-particle
Fitted PDBs: 7c17
Q-score: 0.278
Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O'Halloran TV, Zhang Y
Nat Chem Biol (2021) 17 pp. 57-64 [ DOI: doi:10.1038/s41589-020-00653-x Pubmed: 32989300 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna (72-mer) (22 kDa, DNA from synthetic construct)
- Dna (72-mer) (22 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Silver ion (107 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Hth-type transcriptional regulator cuer (15 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli cuer transcription activation complex with fully duplex promoter dna (507 kDa, Complex from Escherichia coli K-12)
Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 6lcp
Q-score: 0.496
Protein Cell (2020) 11 pp. 458-463 [ Pubmed: 32303992 DOI: doi:10.1007/s13238-020-00712-y ]
- Cdc50 (46 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Heterodimer of dnf1-cdc50 (Complex from Chaetomium thermophilum var. thermophilum DSM 1495)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Phospholipid-transporting atpase (175 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6lcr
Q-score: 0.458
Protein Cell (2020) 11 pp. 458-463 [ Pubmed: 32303992 DOI: doi:10.1007/s13238-020-00712-y ]
- Cdc50 (46 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Heterodimer of dnf1-cdc50 (Complex from Chaetomium thermophilum var. thermophilum DSM 1495)
- Magnesium ion (24 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Phospholipid-transporting atpase (175 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
cryo-EM structure of Escherichia coli Crl transcription activation complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6kj6
Q-score: 0.479
Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y
eLife (2019) 8 [ DOI: doi:10.7554/eLife.50928 Pubmed: 31846423 ]
- Rna (5'-r(*cp*up*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna (51-mer) (15 kDa, DNA from synthetic construct)
- Sigma factor-binding protein crl (16 kDa, Protein from Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks))
- Escherichia coli crl transcription activation complex(crl-tac) (440 kDa, Complex from Escherichia coli K-12)
- Rna polymerase sigma factor rpos (38 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna (51-mer) (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
RNA polymerase II elongation complex arrested at a CPD lesion
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6o6c
Q-score: 0.435
Lahiri I, Xu J, Han BG, Oh J, Wang D, DiMaio F, Leschziner AE
J Struct Biol (2019) 207 pp. 270-278 [ DOI: doi:10.1016/j.jsb.2019.06.004 Pubmed: 31200019 ]
- Rna polymerase ii elongation complex stalled at a cpd lesion (Complex from Saccharomyces cerevisiae)
- Rna (5'-r(p*ap*up*cp*gp*ap*gp*ap*gp*g)-3') (2 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*gp*gp*ap*gp*ap*ap*gp*gp*ap*gp*cp*ap*gp*ap*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna (27-mer) (8 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
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))