Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8a3y
Q-score: 0.231
Farnung L, Ochmann M, Garg G, Vos SM, Cramer P
Mol Cell (2022) 82 pp. 3126-3134.e7 [ Pubmed: 35858621 DOI: doi:10.1016/j.molcel.2022.06.027 ]
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit d (16 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)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein leo1 (210 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Spt6 (117 kDa, Protein from Homo sapiens)
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 ]
- Histone h3.3c (15 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Integrator complex subunit 15 (50 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)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor c/d (65 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 Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Nucleosome (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dsif (Complex from Trichoplusia ni)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex and nelf (Complex from Homo sapiens)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Rna and dna (Complex from Sus scrofa)
- Non-template dna (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (56 kDa, DNA from synthetic construct)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Pre-termination complex (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- 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)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- 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)
- Unk-unk-unk-unk-unk-unk-unk-unk (698 Da, Protein from Sus scrofa)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
RNA polymerase II-Spt4/5-nucleosome-Chd1 structure
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nkx
Q-score: 0.444
Farnung L, Ochmann M, Engeholm M, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 382-387 [ Pubmed: 33846633 DOI: doi:10.1038/s41594-021-00578-6 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Rna (21 kDa, RNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii-spt4/5-chd1-nucleosome (Complex)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (116 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (139-mer) (56 kDa, DNA from synthetic construct)
- Dna (128-mer) (54 kDa, DNA from synthetic construct)
RNA Polymerase II-Spt4/5-nucleosome-FACT structure
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7nky
Q-score: 0.358
Farnung L, Ochmann M, Engeholm M, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 382-387 [ Pubmed: 33846633 DOI: doi:10.1038/s41594-021-00578-6 ]
- Transcription elongation factor spt5 (Complex from Saccharomyces cerevisiae)
- Dna (148-mer) (45 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna (138-mer) (Complex)
- Fact complex subunit spt16 (118 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (Complex from Saccharomyces cerevisiae)
- Rna (5'-r(p*up*cp*up*up*up*up*ap*up*up*up*up*up*up*cp*up*g)-3') (Complex)
- Fact complex subunit spt16 (Complex from Saccharomyces cerevisiae)
- Fact complex subunit pob3 (63 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (148-mer) (Complex)
- Dna-directed rna polymerase ii subunit rpb11 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna (138-mer) (42 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (Complex from Saccharomyces cerevisiae)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Complex from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (Complex from Xenopus laevis)
- Rna (5'-r(p*up*cp*up*up*up*up*ap*up*up*up*up*up*up*cp*up*g)-3') (4 kDa, RNA from synthetic RNA)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin elongation factor spt4 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Complex from Saccharomyces cerevisiae)
- Chromatin elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Complex)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Fact complex subunit pob3 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Complex of rna polymerase ii-spt4/5-fact-nucleosome (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (Complex from Xenopus laevis)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb4 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (Complex from Saccharomyces cerevisiae)
Nucleosome-CHD4 complex structure (single CHD4 copy)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ryr
Q-score: 0.52
Farnung L, Ochmann M, Cramer P
eLife (2020) 9 [ Pubmed: 32543371 DOI: doi:10.7554/eLife.56178 ]
- Dna (Complex from synthetic construct)
- Dna (149-mer) (46 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 4,chromodomain-helicase-dna-binding protein 4,chromodomain-helicase-dna-binding protein 4 (219 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chd4 (Complex from Homo sapiens)
- Nucleosome-chd4 complex (Complex)
- Dna (149-mer) (45 kDa, DNA from synthetic construct)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
Nucleosome-CHD4 complex structure (two CHD4 copies)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6ryu
Q-score: 0.342
Farnung L, Ochmann M, Cramer P
eLife (2020) 9 [ Pubmed: 32543371 DOI: doi:10.7554/eLife.56178 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna (149-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Histone (Complex from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 4 (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (149-mer) (46 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 4,chd4,chromodomain-helicase-dna-binding protein 4 (219 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Nucleosome-chd4 complex (Complex)