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 ]
- 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)
Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9j0n
Q-score: 0.316
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*cp*c)-3') (13 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0o
Q-score: 0.313
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0p
Q-score: 0.311
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)