DNA-directed RNA polymerase with transcriptional activator PafBC
Schilling CM, Zdanowicz R, Rabl J, Muller AU, Boehringer D, Glockshuber R, Weber-Ban E
Sci Adv (2025) 11 pp. eadq9054-eadq9054 [ Pubmed: 39919186 DOI: doi:10.1126/sciadv.adq9054 ]
- Dna-directed rna polymerase with transcriptional activator pafbc (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta' (Protein from Mycolicibacterium smegmatis MC2 155)
- Pafc (Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (Protein from Mycolicibacterium smegmatis MC2 155)
- Pafb (Protein from Mycolicibacterium smegmatis MC2 155)
- Reca-op template strand (DNA from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (Protein from Mycolicibacterium smegmatis MC2 155)
- Reca-op non-template strand (DNA from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit omega (Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (Protein from Mycolicibacterium smegmatis MC2 155)
Transcriptional activator PafBC bound to mycobacterial RNA polymerase
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 9fnd
Q-score: 0.332
Schilling CM, Zdanowicz R, Rabl J, Muller AU, Boehringer D, Glockshuber R, Weber-Ban E
Sci Adv (2025) 11 pp. eadq9054-eadq9054 [ Pubmed: 39919186 DOI: doi:10.1126/sciadv.adq9054 ]
- Pafc (34 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pafbc (Complex from Mycolicibacterium smegmatis MC2 155)
- Transcriptional activator pafbc bound to mycobacterial rna polymerase (Complex from Mycolicibacterium smegmatis MC2 155)
- Transcriptional regulator-like protein (36 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rnap polymerase sigma factor a and rna polymerase-binding protein rbpa (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase (Complex from Mycolicibacterium smegmatis MC2 155)
Composite map of the mycobacterial PafBC-bound transcription initiation complex
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 9fne
Q-score: 0.415
Schilling CM, Zdanowicz R, Rabl J, Muller AU, Boehringer D, Glockshuber R, Weber-Ban E
Sci Adv (2025) 11 pp. eadq9054-eadq9054 [ Pubmed: 39919186 DOI: doi:10.1126/sciadv.adq9054 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase with transcriptional activator pafbc (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Reca-op non-template strand (21 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Pafc (34 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Transcriptional regulator-like protein (36 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Reca-op template strand (20 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8qn8
Q-score: 0.49
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Helicase (81 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Mycobacterium smegmatis rna polymerase in complex with held, siga and rbpa in state ii (Complex from Mycolicibacterium smegmatis MC2 155)
Mycobacterium smegnatis RNAP open promoter complex with SigmaA and RbpA
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 8qti
Q-score: 0.516
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegnatis rnap open promoter complex with sigmaa and rbpa (Complex from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 50-mer non-template strand (15 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Dna 50-mer template strand (15 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8qu6
Q-score: 0.473
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Mycobacterium smegnatis rna polymerase transcription initiation complex with sigmaa, rbpa, held and an upstream-fork promoter fragment (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Helicase (81 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 31-mer (9 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Dna 22-mer (6 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8r2m
Q-score: 0.459
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegnatis rna polymerase transcription initiation complex with sigmaa, rbpa, held n-terminal domain and an upstream-fork promoter fragment; state iii conformation (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Helicase (81 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 31-mer (9 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Dna 22-mer (6 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 8r3m
Q-score: 0.458
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Helicase (81 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 31-mer (9 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegnatis rna polymerase transcription initiation complex with sigmaa, rbpa, held n-terminal, co and pch loop domain, and an upstream-fork promoter fragment; state iii conformation (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna 22-mer (6 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8r6p
Q-score: 0.466
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 50-mer (15 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegnatis rna polymerase rp2-like transcription initiation complex with sigmaa, rbpa, held n-terminal domain and open promoter dna (Complex from Mycolicibacterium smegmatis MC2 155)
- Dna 50-mer (15 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Helicase (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.89 Å
EM Method: Single-particle
Fitted PDBs: 8r6r
Q-score: 0.308
Koval T, Borah N, Sudzinova P, Brezovska B, Sanderova H, Vankova Hausnerova V, Krenkova A, Hubalek M, Trundova M, Adamkova K, Duskova J, Schwarz M, Wiedermannova J, Dohnalek J, Krasny L, Kouba T
Nat Commun (2024) 15 pp. 8740-8740 [ DOI: doi:10.1038/s41467-024-52891-5 Pubmed: 39384756 ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 50-mer (15 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (128 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor siga (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Dna 50-mer (15 kDa, DNA from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Mycobacterium smegnatis rna polymerase rp2-like transcription initiation complex with sigmaa, rbpa and open promoter dna (Complex from Mycolicibacterium smegmatis MC2 155)