Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome- State 1
Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C
PNAS (2022) 119 pp. e2205691119-e2205691119 [ Pubmed: 36095189 DOI: doi:10.1073/pnas.2205691119 ]
Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 7ud5
Q-score: 0.263
Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C
PNAS (2022) 119 pp. e2205691119-e2205691119 [ DOI: doi:10.1073/pnas.2205691119 Pubmed: 36095189 ]
- Mll1 wrad complex (Complex from Homo sapiens)
- Mll1 wrad complex bound to the ubiquitinated nucleosome (Complex)
- Nucleosome (Complex from Xenopus laevis)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Cdna flj56846, highly similar to zinc finger protein hrx (26 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- Protein dpy-30 homolog (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
Resolution: 3.55 Å
EM Method: Single-particle
Fitted PDBs: 8du4
Q-score: 0.237
Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C
PNAS (2022) 119 pp. e2205691119-e2205691119 [ Pubmed: 36095189 DOI: doi:10.1073/pnas.2205691119 ]
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ubiquitinated nucleosome (Complex from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- Rbbp5-wdr5 complex (Complex from Homo sapiens)
- Rbbp5-wdr5 complex bound to the ubiquitinated nucleosome (Complex)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome- State 3
Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C
PNAS (2022) 119 pp. e2205691119-e2205691119 [ DOI: doi:10.1073/pnas.2205691119 Pubmed: 36095189 ]
Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6nog
Q-score: 0.356
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Poised state dot1l in complex with the h2b-ub nucleosome (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Histone core (Complex from Xenopus laevis)
- Dot1l (Complex from Homo sapiens)
- H2b-ub nucleosome (Complex)
Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 6nqa
Q-score: 0.436
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Dot1l (Complex from Xenopus laevis)
- Active state dot1l in complex with the h2b-ub nucleosome (Complex)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone core (Complex from Xenopus laevis)
- H2b-ub nucleosome (Complex)
Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 6nj9
Q-score: 0.551
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- H2h2b-ub nucleosome (Complex)
- Active state dot1l in complex with the h2b-ub nucleosome (Complex)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone core (Complex from Xenopus laevis)
- Dot1l (Complex from Homo sapiens)
RNA Polymerase I elongation complex 1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 5m5x
Q-score: 0.302
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW
Mol Cell (2016) 64 pp. 1135-1143 [ DOI: doi:10.1016/j.molcel.2016.11.013 Pubmed: 27867008 ]
- Rna (6 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Non-template dna (11 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Baker's yeast)
- Transcription scaffold (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Baker's yeast)
- Rna polymerase i elongation complex 1 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
- Template dna (11 kDa, DNA from Saccharomyces cerevisiae)
RNA Polymerase I elongation complex 2
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 5m5y
Q-score: 0.308
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW
Mol Cell (2016) 64 pp. 1135-1143 [ Pubmed: 27867008 DOI: doi:10.1016/j.molcel.2016.11.013 ]
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Baker's yeast)
- Rna polymerase i elongation complex 2 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Baker's yeast)
- Non-template dna (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Transcription scaffold (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Template dna (21 kDa, DNA from Saccharomyces cerevisiae)
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
RNA Polymerase I elongation complex with A49 tandem winged helix domain
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 5m64
Q-score: 0.266
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW
Mol Cell (2016) 64 pp. 1135-1143 [ Pubmed: 27867008 DOI: doi:10.1016/j.molcel.2016.11.013 ]
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Non-template dna (22 kDa, DNA from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Baker's yeast)
- Rna polymerase i elongation complex with a49 tandem winged helix domain (600 kDa, Complex from Saccharomyces cerevisiae)
- Template dna (21 kDa, DNA from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Baker's yeast)
- Transcription scaffold (10 kDa, Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Baker's yeast)
- Rna (3 kDa, RNA from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Baker's yeast)