Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9er2
Q-score: 0.448
van den Heuvel D, Rodriguez-Martinez M, van der Meer PJ, Nieto Moreno N, Park J, Kim HS, van Schie JJM, Wondergem AP, D'Souza A, Yakoub G, Herlihy AE, Kashyap K, Boissiere T, Walker J, Mitter R, Apelt K, de Lint K, Kirdok I, Ljungman M, Wolthuis RMF, Cramer P, Scharer OD, Kokic G, Svejstrup JQ, Luijsterburg MS
Cell (2024) 187 pp. 7107- [ DOI: doi:10.1016/j.cell.2024.10.018 Pubmed: 39547229 ]
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Ts (15 kDa, DNA from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Pol ii-tcr-stk19 (Complex from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Isoform 1 of inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor 1 homolog (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*cp*ap*ap*ap*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (4 kDa, RNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
Type I-FHNH Cascade-dsDNA intermediate complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ydb
Q-score: 0.443
Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z
Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]
- Cas8f fusion with hnh (39 kDa, Protein from Selenomonas sp.)
- Type i-fhnh cascade-dsdna intermediate complex (Complex from Selenomonas sp.)
- Cas5f (28 kDa, Protein from Selenomonas sp.)
- Nts (3 kDa, Macromolecule from Selenomonas sp.)
- Cas6f (20 kDa, Protein from Selenomonas sp.)
- Ts (10 kDa, Macromolecule from Selenomonas sp.)
- Cas7f (38 kDa, Protein from Selenomonas sp.)
- 60-nt crrna (19 kDa, RNA from Selenomonas sp.)
Type I-FHNH Cascade-dsDNA R-loop complex
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8yeo
Q-score: 0.432
Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z
Mol Cell (2024) 84 pp. 3141- [ Pubmed: 39047725 DOI: doi:10.1016/j.molcel.2024.06.033 ]
- Cas8f fusion with hnh (39 kDa, Protein from Selenomonas sp.)
- Cas5f (28 kDa, Protein from Selenomonas sp.)
- Nts (3 kDa, Macromolecule from Selenomonas sp.)
- Cas6f (20 kDa, Protein from Selenomonas sp.)
- Type i-fhnh cascade-dsdna r-loop complex (Complex from Selenomonas sp.)
- Cas7f (38 kDa, Protein from Selenomonas sp.)
- 60-nt crrna (19 kDa, RNA from Selenomonas sp.)
- Ts (15 kDa, Macromolecule from Selenomonas sp.)
Cryo-EM structure of Cas12j-SF05-crRNA-dsDNA complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8inb
Q-score: 0.489
Duan Z, Zhang X, Zhang JT, Li S, Liu R, Sun J, Zhao Q, Jia N, Jia N, Zhu JK
Cell Discov (2023) 9 pp. 117-117 [ DOI: doi:10.1038/s41421-023-00612-5 Pubmed: 37990011 ]
- Nts-dna (16 kDa, DNA from Biggievirus Mos11)
- Ternary complex of cas12j-sf05 with crrna and target dsdna (Complex from Biggievirus Mos11)
- Crrna (18 kDa, RNA from Biggievirus Mos11)
- Ts-dna (16 kDa, DNA from Biggievirus Mos11)
- Cas12j-sf05 (83 kDa, Protein from Biggievirus Mos11)
Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8tug
Q-score: 0.382
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (42 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of cpd lesion containing rna polymerase ii elongation complex with rad26 (engaged state) (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from synthetic construct)
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8tvp
Q-score: 0.357
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of cpd lesion containing rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from synthetic construct)
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8tvq
Q-score: 0.247
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Cryo-em structure of cpd lesion containing 10 subunit rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from synthetic construct)
- Dna repair and recombination protein rad26 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of backtracked Pol II in complex with Rad26
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8tvs
Q-score: 0.305
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of backtracked rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of backtracked Pol II
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8tvv
Q-score: 0.37
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rna (5 kDa, RNA from synthetic construct)
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of backtracked rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of CPD-stalled Pol II (conformation 1)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8tvw
Q-score: 0.385
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of rna polymerase ii elongation complex containing cpd lesion (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)