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 [ DOI: doi:10.1038/s41586-024-07269-4 Pubmed: 38570683 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Template dna (56 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Histone h2a type 1 (14 kDa, Protein from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Pre-termination complex (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Unk-unk-unk-unk-unk-unk-unk-unk (698 Da, Protein from Sus scrofa)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator-pp2a complex and nelf (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Nucleosome (Complex from Homo sapiens)
- Dsif (Complex from Trichoplusia ni)
- Zinc ion (65 Da, Ligand)
- 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Non-template dna (45 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- 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)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 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 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 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 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 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 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structural basis of Integrator-mediated transcription regulation
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7pks
Q-score: 0.278
Fianu I, Chen Y, Dienemann C, Dybkov O, Linden A, Urlaub H, Cramer P
Science (2021) 374 pp. 883-887 [ DOI: doi:10.1126/science.abk0154 Pubmed: 34762484 ]
- Unknown (2 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Rpbi c-terminal domain peptide (1 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Dsif (Complex from Homo sapiens)
- Nelf (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna (Complex from Human immunodeficiency virus 1)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Template dna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)