Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8u8v
Q-score: 0.405
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Substrate atp bound to insertion site (is) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
Cryo-EM Structure of the TEFM-bound Human Mitochondrial Transcription Substrate Rejection Complex
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Template strand dna (ts31mt_+1a) (10 kDa, DNA from synthetic construct)
- Structure of the transcription elongation complex of human mitochondrial polymerase with the closed conformation of the fingers domain (227 kDa, Complex from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Non-template strand dna (nt27mt_+1t) (10 kDa, DNA from synthetic construct)
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Non-cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Template strand dna (ts31mt_+1a) (10 kDa, DNA from synthetic construct)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Non-template strand dna (nt27mt_+1t) (10 kDa, DNA from synthetic construct)
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 (ts) (14 kDa, DNA from synthetic construct)
- Cryo-em structure of cpd lesion containing rna polymerase ii elongation complex with rad26 (engaged state) (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (42 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 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 rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
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 (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 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 rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of cpd lesion containing rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
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 (ts) (14 kDa, DNA from synthetic construct)
- Dna repair and recombination protein rad26 (36 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)
- Rna (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of cpd lesion containing 10 subunit rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
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 (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 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 rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of backtracked rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (nts) (14 kDa, DNA from synthetic construct)
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 (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 polymerase ii subunit rpb7 (19 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)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Cryo-em structure of backtracked rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 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-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 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)
- Rna (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Cryo-em structure of rna polymerase ii elongation complex containing cpd lesion (Complex from Saccharomyces cerevisiae)
- Dna (ts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)