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 (5 kDa, RNA from synthetic construct)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Integrator-pp2a complex and nelf (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 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)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna and dna (Complex from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Homo sapiens)
- Dsif (Complex from Trichoplusia ni)
- Histone h3.3c (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- 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)
- Zinc ion (65 Da, Ligand)
- Pre-termination complex (1 MDa, Complex)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (45 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Template dna (56 kDa, DNA from synthetic construct)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unk-unk-unk-unk-unk-unk-unk-unk (698 Da, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
Structure of Integrator-PP2A-SOSS-CTD post-termination complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8rbz
Q-score: 0.293
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 ]
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 3 (118 kDa, Protein from Homo sapiens)
- Post-termination complex (1 MDa, Complex)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex and nabp2 and inip (Complex from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Unk-unk-unk-unk-unk-unk-unk-unk-unk (783 Da, 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 7 (107 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (1 kDa, Protein from Sus scrofa)
- Soss complex subunit c (11 kDa, Protein from Homo sapiens)
- Soss complex subunit b1 (22 kDa, Protein from Homo sapiens)
- Rna polymerase ii c-terminal domain peptides (Complex from Sus scrofa)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Dss1 (Complex from Trichoplusia ni)
Structure of Integrator-PP2A complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8rc4
Q-score: 0.036
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 ]
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex (Complex from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Integrator complex subunit 6 (101 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex (1 MDa, Complex)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Dss1 (Complex from Trichoplusia ni)
Cryo-EM structure of the PP2A:B55-FAM122A complex, B55 body
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 8twe
Q-score: 0.592
Padi SKR, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W
Nature (2024) 625 pp. 195-203 [ Pubmed: 38123684 DOI: doi:10.1038/s41586-023-06870-3 ]
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (64 kDa, Protein from Homo sapiens)
- Ppp2r1a-ppp2r2a-interacting phosphatase regulator 1 (10 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 55 kda regulatory subunit b alpha isoform (52 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Quadruple complex of pp2a:b55 (pp2aa:pp2ac:b55) bound to fam122a (Complex)
Cryo-EM structure of the PP2A:B55-FAM122A complex, PP2Ac body
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8twi
Q-score: 0.499
Padi SKR, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W
Nature (2024) 625 pp. 195-203 [ Pubmed: 38123684 DOI: doi:10.1038/s41586-023-06870-3 ]
- 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 (64 kDa, Protein from Homo sapiens)
- Ppp2r1a-ppp2r2a-interacting phosphatase regulator 1 (10 kDa, Protein from Homo sapiens)
- Quadruple complex of pp2a:b55 (pp2aa:pp2ac:b55) bound to fam122a (Complex)
- Fe (iii) ion (55 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the PP2A:B55-FAM122A complex
Resolution: 2.79961 Å
EM Method: Single-particle
Fitted PDBs: 8so0
Q-score: 0.561
Padi SKR, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W
Nature (2024) 625 pp. 195-203 [ Pubmed: 38123684 DOI: doi:10.1038/s41586-023-06870-3 ]
- 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 (64 kDa, Protein from Homo sapiens)
- Ppp2r1a-ppp2r2a-interacting phosphatase regulator 1 (10 kDa, Protein from Homo sapiens)
- Quadruple complex of pp2a:b55 (pp2aa:pp2ac:b55) bound to fam122a (Complex)
- Fe (iii) ion (55 Da, Ligand)
- Serine/threonine-protein phosphatase 2a 55 kda regulatory subunit b alpha isoform (52 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the PP2A:B55-ARPP19 complex
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8ttb
Q-score: 0.564
Padi SKR, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W
Nature (2024) 625 pp. 195-203 [ Pubmed: 38123684 DOI: doi:10.1038/s41586-023-06870-3 ]
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (64 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Camp-regulated phosphoprotein 19 (12 kDa, Protein from Homo sapiens)
- Quadruple complex of pp2a:b55 (pp2aa:pp2ac:b55) bound to thiophosphorylated arpp19 (165 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Serine/threonine-protein phosphatase 2a 55 kda regulatory subunit b alpha isoform (52 kDa, Protein from Homo sapiens)
- Fe (iii) ion (55 Da, Ligand)
The structure of the PP2A-B56gamma1 holoenzyme-PME-1 complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7soy
Q-score: 0.319
Li Y, Balakrishnan VK, Rowse M, Wu CG, Bravos AP, Yadav VK, Ivarsson Y, Strack S, Novikova IV, Xing Y
eLife (2022) 11 [ Pubmed: 35924897 DOI: doi:10.7554/eLife.79736 ]
- The structure of pp2a-b56gamma holoenzyme-pme-1 complex (Complex from Homo sapiens)
- 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)
- Isoform gamma-1 of serine/threonine-protein phosphatase 2a 56 kda regulatory subunit gamma isoform (52 kDa, Protein from Homo sapiens)
- Protein phosphatase methylesterase 1 (42 kDa, Protein from Homo sapiens)
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 [ Pubmed: 34762484 DOI: doi:10.1126/science.abk0154 ]
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from domestic pig)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from domestic pig)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from domestic pig)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Rpbi c-terminal domain peptide (1 kDa, Protein from domestic pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from domestic pig)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from domestic pig)
- Manganese (ii) ion (54 Da, Ligand)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from domestic pig)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from domestic pig)
- Magnesium ion (24 Da, Ligand)
- Unknown (2 kDa, Protein from Homo sapiens)
- Rna (Complex from Human immunodeficiency virus 1)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from domestic pig)
- Template dna (Complex from Human immunodeficiency virus 1)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from domestic pig)
- Rna polymerase ii subunit k (7 kDa, Protein from domestic pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from domestic pig)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from domestic pig)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dsif (Complex from Homo sapiens)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Nelf (Complex from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ouf
Q-score: 0.431
Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN
Nat Commun (2021) 12 pp. 4996-4996 [ Pubmed: 34404793 DOI: doi:10.1038/s41467-021-25284-1 ]
- Dna (5'-d(*ap*cp*tp*gp*tp*gp*tp*tp*tp*gp*gp*cp*gp*cp*tp*tp*cp*tp*cp*tp*c)-3') (9 kDa, DNA from Simian T-lymphotropic virus 1)
- 4-azanyl-~{n}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[3-(dimethylamino)-3-oxidanylidene-propyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide (445 Da, Ligand)
- Complex of stlv-1 marb43 integrase with nascent viral dna, the human pp2a b56 subunit and the drug inhibitor xz450 (331 kDa, Complex)
- Integrase (33 kDa, Protein from Simian T-lymphotropic virus 1)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(*gp*ap*gp*ap*gp*ap*ap*gp*cp*gp*cp*cp*ap*ap*ap*cp*ap*cp*a)-3') (8 kDa, DNA from Simian T-lymphotropic virus 1)
- Isoform 3 of pc4 and sfrs1-interacting protein,isoform gamma-1 of serine/threonine-protein phosphatase 2a 56 kda regulatory subunit gamma isoform (80 kDa, Protein from Homo sapiens)