Structure of Sen1 bound RNA Polymerase II pre-termination complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ram
Q-score: 0.394
Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01409-0 Pubmed: 39424994 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rna (11 kDa, RNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Sen1 bound rna polymerase ii pre-termination complex (Complex)
- Zinc ion (65 Da, Ligand)
- Non-template strand (17 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor 1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (18 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factors (Complex from Saccharomyces cerevisiae)
- Helicase sen1 (252 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna and rna (Complex from Human immunodeficiency virus 2)
- Transcription elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8rap
Q-score: 0.24
Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01409-0 Pubmed: 39424994 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Beryllium trifluoride ion (66 Da, Ligand)
- Rna (11 kDa, RNA from Human immunodeficiency virus 2)
- Tertiary complex of rna polymerase ii with elongation factors elf1, spt4, spt5 and the termination factor sen1 (Complex)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii (Complex from Saccharomyces cerevisiae)
- Non-template strand (17 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor 1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Template strand (18 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex from Human immunodeficiency virus 2)
- Rna (Complex from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factors (Complex from Saccharomyces cerevisiae)
- Helicase sen1 (252 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8rbx
Q-score: 0.037
Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P
Nature (2024) 629 pp. 219-227 [ Pubmed: 38570683 DOI: doi:10.1038/s41586-024-07269-4 ]
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Non-template dna (45 kDa, DNA from synthetic construct)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Pre-termination complex (1 MDa, Complex)
- Unk-unk-unk-unk-unk-unk-unk-unk (698 Da, Protein from Sus scrofa)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Dsif (Complex from Trichoplusia ni)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk (1 kDa, Protein from Homo sapiens)
- Rna and dna (Complex from Sus scrofa)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Template dna (56 kDa, DNA from synthetic construct)
- Nelf-b,negative elongation factor b,negative elongation factor b,negative elongation factor b,negative elongation factor b,negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex and nelf (Complex from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Homo sapiens)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Nucleosome (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
Structure of the mammalian Pol II-SPT6 complex, Struture 4 (Global map)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Transcription elongation factor spt6 (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Rpb3 (Protein from Sus scrofa)
- Rpb9 (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Spt6h (Protein from Homo sapiens)
- Eloa1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Eloc (Protein from Homo sapiens)
- Rpb6 (Protein from Sus scrofa)
- Rpb1 (Protein from Sus scrofa)
- Rpb4 (Protein from Sus scrofa)
- Rpb5 (Protein from Sus scrofa)
- Rpb8 (Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rpb2 (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Elob (Protein from Homo sapiens)
- Rpb7 (Protein from Sus scrofa)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Elongin a (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Transcription elongation factor spt6 (Protein from Homo sapiens)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Elongin c (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Elongin b (Protein from Homo sapiens)
- Template dna (DNA from synthetic construct)
Structure of the mammalian Pol II-SPT6 complex (composite map)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8oeu
Q-score: 0.526
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite map 2)
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8oev
Q-score: 0.468
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8oew
Q-score: 0.56
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Structure of the mammalian Pol II-SPT6-Elongin complex, Structure 1 (local resolution filtered map)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8of0
Q-score: 0.422
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)