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 ]
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 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)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein leo1 (210 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- 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)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Spt6 (117 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 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)
Rpd3S bound to an H3K36Cme3 modified nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8tof
Q-score: 0.464
Nat Commun (2023) 14 pp. 8128-8128 [ Pubmed: 38065958 DOI: doi:10.1038/s41467-023-43968-8 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (63 kDa, DNA from synthetic construct)
- Dna (176-mer) (66 kDa, DNA from synthetic construct)
- Rco1 (515 Da, Protein from Saccharomyces cerevisiae)
- Histone n-terminal tail (657 Da, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpd3s bound to h3k36cme3 nucleosome (Complex)
Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7unc
Q-score: 0.344
Filipovski M, Soffers JHM, Vos SM, Farnung L
Science (2022) 376 pp. 1313-1316 [ Pubmed: 35709268 DOI: doi:10.1126/science.abo3851 ]
- Pol ii-dsif-spt6-paf1c-tfiis complex with rewrapped nucleosome (Complex)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpol4c domain-containing protein (20 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Non-template dna (64 kDa, DNA from synthetic construct)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rpb8 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7und
Q-score: 0.216
Filipovski M, Soffers JHM, Vos SM, Farnung L
Science (2022) 376 pp. 1313-1316 [ Pubmed: 35709268 DOI: doi:10.1126/science.abo3851 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Pol ii-dsif-spt6-paf1c-tfiis complex (stalled at +38) (Complex)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpol4c domain-containing protein (20 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Non-template dna (64 kDa, DNA from synthetic construct)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rpb8 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
Structure of transcribing RNA polymerase II-nucleosome complex
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 6i84
Q-score: 0.241
Nat Commun (2018) 9 pp. 5432-5432 [ DOI: doi:10.1038/s41467-018-07870-y Pubmed: 30575770 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (158-mer) (49 kDa, DNA from synthetic construct)
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (3 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (170-mer) (52 kDa, DNA from synthetic construct)
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex)
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Structure of nucleosome-Chd1 complex
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 5o9g
Q-score: 0.018
Farnung L, Vos SM, Wigge C, Cramer P
Nature (2017) 550 pp. 539-542 [ Pubmed: 29019976 DOI: doi:10.1038/nature24046 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Protein-nucleic acid complex (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (162-mer) (64 kDa, DNA from synthetic construct)
- Protein-nucleic acid complex (Complex from Saccharomyces cerevisiae S288c)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Protein-nucleic acid complex (Complex from synthetic construct)
- Protein-nucleic acid complex (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (162-mer) (64 kDa, DNA from synthetic construct)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288c)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)