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 ]
- Protein dpy-30 homolog (11 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
- Mll1 wrad complex bound to the ubiquitinated nucleosome (Complex)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Mll1 wrad complex (Complex from Homo sapiens)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Cdna flj56846, highly similar to zinc finger protein hrx (26 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 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 [ DOI: doi:10.1073/pnas.2205691119 Pubmed: 36095189 ]
- Rbbp5-wdr5 complex (Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 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)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Ubiquitinated nucleosome (Complex from Xenopus laevis)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- Rbbp5-wdr5 complex bound to the ubiquitinated nucleosome (Complex)
Nucleosome with TBP and TFIIA bound at SHL -6
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7oh9
Q-score: 0.49
PNAS (2021) 118 [ Pubmed: 34301908 DOI: doi:10.1073/pnas.2108859118 ]
- Nucleosome with tbp and tfiia (230 kDa, Complex)
- Histone octamer (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Dna (145-mer) (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Tbp (Complex from Saccharomyces cerevisiae)
- Tfiia (Complex from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
nucleosome with TBP and TFIIA bound at SHL +2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7oha
Q-score: 0.516
PNAS (2021) 118 [ Pubmed: 34301908 DOI: doi:10.1073/pnas.2108859118 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (122-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (122-mer) (44 kDa, DNA from synthetic construct)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Nucleosome with tbp (230 kDa, Complex)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ohb
Q-score: 0.435
PNAS (2021) 118 [ Pubmed: 34301908 DOI: doi:10.1073/pnas.2108859118 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nucleosome with tbp (230 kDa, Complex)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7ohc
Q-score: 0.587
PNAS (2021) 118 [ Pubmed: 34301908 DOI: doi:10.1073/pnas.2108859118 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nucleosome core particle (200 kDa, Complex)