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)
RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iie (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- General transcription factor iib (Complex from Homo sapiens)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8byq
Q-score: 0.187
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- 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)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih (Complex from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iie (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iib (Complex from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8bz1
Q-score: 0.244
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- 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)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii core pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Zinc ion (65 Da, Ligand)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iib (Complex from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
The 4x177 nucleosome array containing H1
Resolution: 9.5 Å
EM Method: Single-particle
Fitted PDBs: 7pet
Q-score: 0.105
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Tetranucleosome from 4x177 nucleosome array (Complex)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (702-mer) (218 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (702-mer) (215 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Trinucleosome of the 4x177 nucleosome array containing H1
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 7peu
Q-score: 0.138
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (522-mer) (160 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (522-mer) (161 kDa, DNA from synthetic construct)
- Trinucleosome from 4x177 nucleosome array (Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Nucleosome stack of the 4x177 nucleosome array containing H1
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 7pev
Q-score: 0.224
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (520-mer) (218 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Nucleosome stack from 4x177 nucleosome array (Complex)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Dna (520-mer) (215 kDa, DNA from Homo sapiens)
Nucleosome 1 of the 4x177 nucleosome array containing H1
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7pew
Q-score: 0.29
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (176-mer) (53 kDa, DNA from synthetic construct)
- Nucleosome 1 from 4x177 nucleosome array (Complex)
- Dna (176-mer) (54 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
Nucleosome 2 of the 4x177 nucleosome array containing H1
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7pex
Q-score: 0.267
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Nucleosome 2 from 4x177 nucleosome array (Complex)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (177-mer) (55 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Nucleosome 3 of the 4x177 nucleosome array containing H1
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7pey
Q-score: 0.281
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosome 3 from 4x177 nucleosome array (Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Dna (203-mer) (53 kDa, DNA from synthetic construct)
- Dna (202-mer) (52 kDa, DNA from synthetic construct)