Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Free stalled human rna polymerase ii elongation complex in an intermediate translocation state (430 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Stalled human rna polymerase ii elongation complex bound to an apo recql5 helicase (490 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Atp-dependent dna helicase q5 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Atp-dependent dna helicase q5 (109 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Stalled human rna polymerase ii elongation complex bound to an amppnp-bound recql5 helicase (490 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Atp-dependent dna helicase q5 (109 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Stalled human rna polymerase ii elongation complex bound to an adp-bound recql5 helicase (490 kDa, Complex from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
Shi J, Feng Z, Song Q, Wen A, Liu T, Xu L, Ye Z, Xu S, Gao F, Xiao L, Zhu J, Das K, Zhao G, Li J, Feng Y, Lin W
Nat Commun (2025) 16 pp. 1573- [ DOI: doi:10.1038/s41467-025-56697-x ]
- Mycobacterium tuberculosis transcription activation complex with unphosphated phop (Complex from Mycobacterium tuberculosis)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis)
- Template strand dna (33 kDa, DNA from Mycobacterium tuberculosis)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis)
- Non-template strand dna (33 kDa, DNA from Mycobacterium tuberculosis)
- Rna polymerase sigma factor siga (57 kDa, Protein from Mycobacterium tuberculosis)
Shi J, Feng Z, Song Q, Wen A, Liu T, Xu L, Ye Z, Xu S, Gao F, Xiao L, Zhu J, Das K, Zhao G, Li J, Feng Y, Lin W
Nat Commun (2025) 16 pp. 1573- [ DOI: doi:10.1038/s41467-025-56697-x ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Possible two component system response transcriptional positive regulator phop (30 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor siga (57 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Mycobacterium tuberculosis transcription activation complex with two phop molecules (Complex from Mycobacterium tuberculosis)
- Template strand dna (23 kDa, DNA from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Non-template strand dna (23 kDa, DNA from Mycobacterium tuberculosis H37Rv)
Shi J, Feng Z, Song Q, Wen A, Liu T, Xu L, Ye Z, Xu S, Gao F, Xiao L, Zhu J, Das K, Zhao G, Li J, Feng Y, Lin W
Nat Commun (2025) 16 pp. 1573- [ DOI: doi:10.1038/s41467-025-56697-x ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor siga (57 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Mycobacterium tuberculosis transcription activation complex with four phop molecules (composite map) (Complex from Mycobacterium tuberculosis)
- Template strand dna of the promoter (30 kDa, DNA from Mycobacterium tuberculosis H37Rv)
- Possible two component system response transcriptional positive regulator phop (27 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Non-template strand dna of the promoter (30 kDa, DNA from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
Shi J, Feng Z, Song Q, Wen A, Liu T, Xu L, Ye Z, Xu S, Gao F, Xiao L, Zhu J, Das K, Zhao G, Li J, Feng Y, Lin W
Nat Commun (2025) 16 pp. 1573- [ DOI: doi:10.1038/s41467-025-56697-x ]
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Template strand dna of the promoter (33 kDa, DNA from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor siga (57 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Mycobacterium tuberculosis transcription activation complex with six phop molecules (composite map) (Complex from Mycobacterium tuberculosis)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Possible two component system response transcriptional positive regulator phop (27 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Non-template strand dna of the promoter (33 kDa, DNA from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 9mu9
Q-score: 0.202
Venette-Smith NL, Vishwakarma RK, Dollinger R, Schultz J, Venkatakrishnan V, Babitzke P, Anand G, Gilmour DS, Armache J-P, Murakami K
To Be Published
- Non-template dna (50 kDa, DNA from Drosophila melanogaster)
- Rna (3 kDa, RNA from Drosophila melanogaster)
- Template dna (53 kDa, DNA from Drosophila melanogaster)
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (9 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb12 (5 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Drosophila melanogaster)
- Native purified nucleosome elongation complex from drosophila melanogaster (750 kDa, Complex from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb2 (132 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb1 (166 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb9 (13 kDa, Protein from Drosophila melanogaster)
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 [ DOI: doi:10.1126/sciadv.adq9054 Pubmed: 39919186 ]
- Dna-directed rna polymerase subunit alpha (Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase-binding protein rbpa (Protein from Mycolicibacterium smegmatis MC2 155)
- Reca-op template strand (DNA from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta' (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 (Protein from Mycolicibacterium smegmatis MC2 155)
- Pafb (Protein from Mycolicibacterium smegmatis MC2 155)
- Rna polymerase sigma factor siga (Protein from Mycolicibacterium smegmatis MC2 155)
- Reca-op non-template strand (DNA from Mycolicibacterium smegmatis MC2 155)
- Dna-directed rna polymerase subunit beta (Protein from Mycolicibacterium smegmatis MC2 155)
- Pafc (Protein from Mycolicibacterium smegmatis MC2 155)