Cryo-EM structure of CII-dependent transcription activation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8igr
Q-score: 0.52
Zhao M, Gao B, Wen A, Feng Y, Lu YQ
Structure (2023) 31 pp. 968- [ DOI: doi:10.1016/j.str.2023.05.008 Pubmed: 37269829 ]
- Template strand dna (26 kDa, DNA from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Cii-dependent transcription activation complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Transcriptional activator ii (11 kDa, Protein from Escherichia phage Lambda)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Nontemplate strand dna (26 kDa, DNA from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
Cryo-EM structure of Synechocystis sp. PCC 6803 RPitc
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8gzg
Q-score: 0.488
Shen L, Lai G, You L, Shi J, Wu X, Puiu M, Gu Z, Feng Y, Yuzenkova Y, Zhang Y
PNAS (2023) 120 pp. e2219290120-e2219290120 [ DOI: doi:10.1073/pnas.2219290120 Pubmed: 37036976 ]
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(*up*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- The complex of synechocystis sp. pcc 6803 rpitc (500 kDa, Complex from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechocystis sp. PCC 6803)
- Template strand dna (20 kDa, DNA from synthetic construct)
- Nontemplate strand dna (20 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Synechocystis sp. PCC 6803)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor siga (50 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta' (145 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechocystis sp. PCC 6803)
Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8gzh
Q-score: 0.534
Shen L, Lai G, You L, Shi J, Wu X, Puiu M, Gu Z, Feng Y, Yuzenkova Y, Zhang Y
PNAS (2023) 120 pp. e2219290120-e2219290120 [ DOI: doi:10.1073/pnas.2219290120 Pubmed: 37036976 ]
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechocystis sp. PCC 6803)
- Template strand dna (20 kDa, DNA from synthetic construct)
- Nontemplate strand dna (20 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Synechocystis sp. PCC 6803)
- The complex of synechocystis sp. pcc 6803 ctp-bound rpitc (500 kDa, Complex from Synechocystis sp. PCC 6803)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor siga (50 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta' (145 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytidine-5'-triphosphate (483 Da, Ligand)
The cryo-EM structure of an AlpA-loading complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7xya
Q-score: 0.447
Wen A, Zhao M, Jin S, Lu YQ, Feng Y
Nucleic Acids Res (2022) 50 pp. 8321-8330 [ Pubmed: 35871295 DOI: doi:10.1093/nar/gkac608 ]
- Rna polymerase sigma factor rpod (69 kDa, Protein from Pseudomonas aeruginosa)
- Template strand dna (19 kDa, DNA from Pseudomonas aeruginosa)
- Magnesium ion (24 Da, Ligand)
- Alpa-loading complex (Complex from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Pseudomonas aeruginosa)
- Nontemplate strand dna (19 kDa, DNA from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit beta (151 kDa, Protein from Pseudomonas aeruginosa)
- Rna (3 kDa, RNA from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Pseudomonas aeruginosa)
- Alpa (20 kDa, Protein from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit beta' (154 kDa, Protein from Pseudomonas aeruginosa)
The cryo-EM structure of an AlpA-loaded complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7xyb
Q-score: 0.381
Wen A, Zhao M, Jin S, Lu YQ, Feng Y
Nucleic Acids Res (2022) 50 pp. 8321-8330 [ Pubmed: 35871295 DOI: doi:10.1093/nar/gkac608 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Pseudomonas aeruginosa)
- Alpa (20 kDa, Protein from Pseudomonas aeruginosa)
- Nontemplate strand dna (24 kDa, DNA from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit beta (151 kDa, Protein from Pseudomonas aeruginosa)
- Template strand dna (23 kDa, DNA from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Pseudomonas aeruginosa)
- Alpa-loaded complex (Complex from Pseudomonas aeruginosa)
- Rna (4 kDa, RNA from Pseudomonas aeruginosa)
- Dna-directed rna polymerase subunit beta' (154 kDa, Protein from Pseudomonas aeruginosa)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6xh7
Q-score: 0.344
Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B
iScience (2021) 24 pp. 102449-102449 [ DOI: doi:10.1016/j.isci.2021.102449 Pubmed: 34113812 ]
- Cuer-tac without rna (530 kDa, Complex from Escherichia coli)
- Nontemplate strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Hth-type transcriptional regulator cuer (16 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
CueR-transcription activation complex with RNA transcript
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6xh8
Q-score: 0.318
Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B
iScience (2021) 24 pp. 102449-102449 [ DOI: doi:10.1016/j.isci.2021.102449 Pubmed: 34113812 ]
- Cuer-tac with rna (540 kDa, Complex from Escherichia coli)
- Nontemplate strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Hth-type transcriptional regulator cuer (16 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Nascent rna (1 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Resolution: 5.0 Å
EM Method: Single-particle
Fitted PDBs: 6m6a
Q-score: 0.256
Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y
Nucleic Acids Res (2020) 48 pp. 11762-11772 [ Pubmed: 33068413 DOI: doi:10.1093/nar/gkaa904 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Template strand dna (19 kDa, DNA from Thermus thermophilus)
- Transcription-repair-coupling factor (109 kDa, Protein from Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (170 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Nontemplate strand dna (19 kDa, DNA from Thermus thermophilus)
- Thermus thermophilus transcription-coupled dna repair complex (Complex from Thermus thermophilus)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6m6b
Q-score: 0.357
Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y
Nucleic Acids Res (2020) 48 pp. 11762-11772 [ Pubmed: 33068413 DOI: doi:10.1093/nar/gkaa904 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Template strand dna (19 kDa, DNA from Thermus thermophilus)
- Transcription-repair-coupling factor (109 kDa, Protein from Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (170 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Thermus thermophilus transcription-repair coupling complex (Complex from Thermus thermophilus)
- Nontemplate strand dna (19 kDa, DNA from Thermus thermophilus)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
CryoEM structure of Thermus thermophilus RNA polymerase elongation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6m6c
Q-score: 0.519
Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y
Nucleic Acids Res (2020) 48 pp. 11762-11772 [ Pubmed: 33068413 DOI: doi:10.1093/nar/gkaa904 ]
- Rna (6 kDa, RNA from Thermus thermophilus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Template strand dna (19 kDa, DNA from Thermus thermophilus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (170 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
- Thermus thermophilus rna polymerase elongation complex (Complex from Thermus thermophilus)
- Nontemplate strand dna (19 kDa, DNA from Thermus thermophilus)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))