Cryo-EM structure of Staphylococcus aureus sigA-dependent RNAP-promoter open complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8x6f
Q-score: 0.388
Yuan L, Liu Q, Xu L, Wu B, Feng Y
Nat Commun (2024) 15 pp. 4850-4850 [ Pubmed: 38844782 DOI: doi:10.1038/s41467-024-49229-6 ]
- Siga-dependent rnap-promoter open complex (Complex from Staphylococcus aureus)
- Rna polymerase sigma factor siga (42 kDa, Protein from Staphylococcus aureus)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Staphylococcus aureus)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Staphylococcus aureus)
- Dna-directed rna polymerase subunit epsilon (8 kDa, Protein from Staphylococcus aureus)
- Dna (71-mer) (21 kDa, DNA from Staphylococcus aureus)
- Dna-directed rna polymerase subunit beta' (135 kDa, Protein from Staphylococcus aureus)
- Dna (71-mer) (21 kDa, DNA from Staphylococcus aureus)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Staphylococcus aureus)
Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8h3v
Q-score: 0.191
Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ
Nat Struct Mol Biol (2024) 31 pp. 293-299 [ DOI: doi:10.1038/s41594-023-01149-7 Pubmed: 38177666 ]
- Full transcription activation complex with two activators ntca and ntcb (718 kDa, Complex from Anabaena)
- Ntca (24 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Rna polymerase sigma factor siga (45 kDa, Protein from Anabaena)
- Ntcb (34 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta' (147 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit gamma (70 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta (126 kDa, Protein from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
Cryo-EM structure of the transcription activation complex NtcA-TAC
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8h40
Q-score: 0.353
Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ
Nat Struct Mol Biol (2024) 31 pp. 293-299 [ Pubmed: 38177666 DOI: doi:10.1038/s41594-023-01149-7 ]
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Anabaena)
- Transcription activation complex with the global regulator ntca (580 kDa, Complex from Anabaena)
- Dna-directed rna polymerase subunit gamma (70 kDa, Protein from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Ntca (24 kDa, Protein from Anabaena)
- Rna polymerase sigma factor siga (45 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Anabaena)
- Dna (125-mer) (38 kDa, DNA from Anabaena)
- Dna-directed rna polymerase subunit beta' (147 kDa, Protein from Anabaena)
- Dna-directed rna polymerase subunit beta (126 kDa, Protein from Anabaena)
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8hih
Q-score: 0.202
Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W
PNAS (2023) 120 pp. e2300282120-e2300282120 [ Pubmed: 37216560 DOI: doi:10.1073/pnas.2300282120 ]
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Transcriptional regulatory protein (27 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis)
- Zinc ion (65 Da, Ligand)
- Mycobacterium tuberculosis transcription initiation complex with transcription factor glnr (Complex from Mycobacterium tuberculosis)
- Rna polymerase sigma factor siga (57 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis)
- Magnesium ion (24 Da, Ligand)
- Non-template strand dna of amtb promoter (33 kDa, DNA from Mycobacterium tuberculosis)
- Template strand dna of amtb promoter (33 kDa, DNA from Mycobacterium tuberculosis)
Cryo-EM structure of Synechocystis sp. PCC 6803 RPitc
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8gzg
Q-score: 0.488
PNAS (2023) [ ]
- Nontemplate strand dna (20 kDa, DNA from synthetic construct)
- Rna (5'-r(*up*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Template strand dna (20 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta' (145 kDa, Protein from Synechocystis sp. PCC 6803)
- The complex of synechocystis sp. pcc 6803 rpitc (500 kDa, Complex from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechocystis sp. PCC 6803)
- Rna polymerase sigma factor siga (50 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit alpha (36 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
PNAS (2023) [ ]
- Template strand dna (20 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Synechocystis sp. PCC 6803)
- Nontemplate strand dna (20 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechocystis sp. PCC 6803)
- Zinc ion (65 Da, Ligand)
- Cytidine-5'-triphosphate (483 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 omega (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- The complex of synechocystis sp. pcc 6803 ctp-bound rpitc (500 kDa, Complex from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechocystis sp. PCC 6803)
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8dy7
Q-score: 0.482
Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA
PNAS (2023) 120 pp. e2220785120-e2220785120 [ DOI: doi:10.1073/pnas.2220785120 Pubmed: 36888660 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Transcriptional regulator whib (10 kDa, Protein from Streptomyces venezuelae)
- Dna (78-mer) (30 kDa, DNA from Streptomyces venezuelae)
- Dna (71-mer) (30 kDa, DNA from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Streptomyces venezuelae)
- Probable cell division protein whia (37 kDa, Protein from Streptomyces venezuelae)
- Rna polymerase sigma factor siga (56 kDa, Protein from Streptomyces venezuelae)
- Rna polymerase-binding protein rbpa (14 kDa, Protein from Streptomyces venezuelae)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Streptomyces venezuelae)
- Streptomyces venezuelae rnap transcription open promoter complex with whia and whib transcription factors (Complex from Streptomyces venezuelae)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8dy9
Q-score: 0.492
Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA
PNAS (2023) 120 pp. e2220785120-e2220785120 [ Pubmed: 36888660 DOI: doi:10.1073/pnas.2220785120 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (38-mer) (15 kDa, DNA from Streptomyces venezuelae)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor siga (56 kDa, Protein from Streptomyces venezuelae)
- Rna polymerase-binding protein rbpa (14 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Streptomyces venezuelae ATCC 10712)
- Probable cell division protein whia (34 kDa, Protein from Streptomyces venezuelae)
- Zinc ion (65 Da, Ligand)
- Dna (38-mer) (15 kDa, DNA from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Streptomyces venezuelae)
- Transcriptional regulator whib (10 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Streptomyces venezuelae)
- Streptomyces venezuelae rnap unconstrained open promoter complex with whia and whib transcription factors (Complex from Streptomyces venezuelae)
Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with one Zur dimers
Resolution: 3.77 Å
EM Method: Single-particle
Fitted PDBs: 7vpd
Q-score: 0.31
Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J
Nucleic Acids Res (2022) 50 pp. 8363-8376 [ Pubmed: 35871291 DOI: doi:10.1093/nar/gkac627 ]
- Dna (84-mer) (25 kDa, DNA from Streptomyces coelicolor A3(2))
- Magnesium ion (24 Da, Ligand)
- Dna (84-mer) (26 kDa, DNA from Streptomyces coelicolor A3(2))
- Zinc ion (65 Da, Ligand)
- Cryo-em structure of streptomyces coelicolor rnap-promoter open complex with one zur dimers (560 kDa, Complex from Streptomyces coelicolor A3(2))
- Putative metal uptake regulation protein (16 kDa, Protein from Streptomyces coelicolor A3(2))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Streptomyces coelicolor A3(2))
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Streptomyces coelicolor A3(2))
- Dna-directed rna polymerase subunit beta' (145 kDa, Protein from Streptomyces coelicolor A3(2))
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Streptomyces coelicolor A3(2))
- Rna polymerase sigma factor siga (58 kDa, Protein from Streptomyces coelicolor A3(2))
Clostridioides difficile RNAP with fidaxomicin
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 7l7b
Q-score: 0.483
Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA
Nature (2022) 604 pp. 541-545 [ DOI: doi:10.1038/s41586-022-04545-z Pubmed: 35388215 ]
- Dna-directed rna polymerase subunit beta' (129 kDa, Protein from Clostridia bacterium)
- Zinc ion (65 Da, Ligand)
- Clostridioides difficile rna polymerase in complex with fidaxomicin (Complex from Clostridia bacterium)
- Dna-directed rna polymerase subunit alpha (34 kDa, Protein from Clostridia bacterium)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Clostridia bacterium)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Clostridia bacterium)
- Rna polymerase sigma factor siga (44 kDa, Protein from Clostridia bacterium)
- Fidaxomicin (1 kDa, Ligand)