Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ssa
Q-score: 0.449
Donovan BT, Chen H, Eek P, Meng Z, Jipa C, Tan S, Bai L, Poirier MG
Mol Cell (2023) 83 pp. 1251-1263.e6 [ DOI: doi:10.1016/j.molcel.2023.03.006 Pubmed: 36996811 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a.1 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Centromere-binding protein 1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (137-mer) (46 kDa, DNA from synthetic construct)
- Centromere-binding protein 1 (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2, histone h4 (Complex from Xenopus laevis)
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a.1, histone h2b.1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Pioneer factor cbf1 in complex with the nucleosome (286 kDa, Complex)
Human menin in complex with H3K79Me2 nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8gpn
Q-score: 0.459
Lin J, Wu Y, Tian G, Yu D, Yang E, Lam WH, Liu Z, Jing Y, Dang S, Bao X, Wong JWH, Zhai Y, Li XD
Science (2023) 379 pp. 717-723 [ Pubmed: 36795828 DOI: doi:10.1126/science.adc9318 ]
- Isoform 2 of menin (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Isoform 2 of menin (67 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (Complex from Homo sapiens)
- Human menin in complex with nh3k79 dimethylated nucleosome (300 kDa, Complex from Xenopus laevis)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nh3k79 dimethylated nucleosome (Complex)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
RNA polymerase II transcribing a chromatosome (type I)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8h0v
Q-score: 0.228
Hirano R, Ehara H, Kujirai T, Uejima T, Takizawa Y, Sekine SI, Kurumizaka H
Nat Commun (2022) 13 pp. 7287-7287 [ DOI: doi:10.1038/s41467-022-35003-z Pubmed: 36435862 ]
- Rna (5'-r(p*ap*gp*cp*ap*ap*up*ap*gp*gp*ap*gp*cp*up*u)-3') (4 kDa, RNA from synthetic construct)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h1.2 (22 kDa, Protein from Homo sapiens)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Rna polymerase ii transcribing a chromatosome (type i) (Complex)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna,rna (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
RNA polymerase II transcribing a chromatosome (type II)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8h0w
Q-score: 0.16
Hirano R, Ehara H, Kujirai T, Uejima T, Takizawa Y, Sekine SI, Kurumizaka H
Nat Commun (2022) 13 pp. 7287-7287 [ DOI: doi:10.1038/s41467-022-35003-z Pubmed: 36435862 ]
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*up*ap*gp*gp*ap*gp*cp*up*up*ap*c)-3') (4 kDa, RNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h1.2 (22 kDa, Protein from Homo sapiens)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Komagataella phaffii)
- Histone (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii transcribing a chromatosome (type ii) (Complex)
- Dna, rna (Complex)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
Cryo-EM structure of human subnucleosome (closed form)
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7x57
Q-score: 0.37
Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H
PNAS (2022) 119 pp. e2206542119-e2206542119 [ Pubmed: 36322721 DOI: doi:10.1073/pnas.2206542119 ]
- Widom601 dna fw (145-mer) (44 kDa, DNA from synthetic construct)
- Widom601 dna rv (145-mer) (44 kDa, DNA from synthetic construct)
- Widom601 dna fw (145-mer),widom601 dna rw (145-mer) (Complex from synthetic construct)
- Histone h3.1,histone h4 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cryo-em structure of human subnucleosome (closed form) (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of human subnucleosome (open form)
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7x58
Q-score: 0.35
Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H
PNAS (2022) 119 pp. e2206542119-e2206542119 [ Pubmed: 36322721 DOI: doi:10.1073/pnas.2206542119 ]
- Widom601 dna fw (145-mer) (44 kDa, DNA from synthetic construct)
- Cryo-em structure of human subnucleosome (open form) (Complex)
- Widom601 dna fw (145-mer),widom601 dna rv (145-mer) (Complex from synthetic construct)
- Widom601 dna rv (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1,histone h4 (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of human subnucleosome (intermediate form)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7yoz
Q-score: 0.246
Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H
PNAS (2022) 119 pp. e2206542119-e2206542119 [ Pubmed: 36322721 DOI: doi:10.1073/pnas.2206542119 ]
- Widom601 dna fw (145-mer) (44 kDa, DNA from synthetic construct)
- Cryo-em structure of human subnucleosome (intermediate form) (Complex)
- Widom601 dna fw (145-mer),widom601 dna rv (145-mer) (Complex from synthetic construct)
- Widom601 dna rv (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.1,histone h4 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 7xzy
Q-score: 0.256
Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H
Pnas Nexus (2022) 1 pp. pgac177-pgac177 [ Pubmed: 36714865 DOI: doi:10.1093/pnasnexus/pgac177 ]
- 193 base-pair dna (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone octamer (Complex)
- Cryo-em structure of the nucleosome containing 193 base-pair dna with a p53 target sequence (239 kDa, Complex from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7y00
Q-score: 0.32
Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H
Pnas Nexus (2022) 1 pp. pgac177-pgac177 [ Pubmed: 36714865 DOI: doi:10.1093/pnasnexus/pgac177 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone octamer (Complex)
- 169 base-pair of dna (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Cryo-em structure of the nucleosome containing 169 base-pair dna with a p53 target sequence (223 kDa, Complex from Homo sapiens)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
RNA polymerase II elongation complex transcribing a nucleosome (EC49B)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7xt7
Q-score: 0.207
Ehara H, Kujirai T, Shirouzu M, Kurumizaka H, Sekine SI
Science (2022) 377 pp. eabp9466-eabp9466 [ DOI: doi:10.1126/science.abp9466 Pubmed: 35981082 ]
- Leo1 (52 kDa, Protein from Komagataella phaffii)
- Constituent of paf1 complex with rna polymerase ii, paf1p, hpr1p, ctr9, leo1, rtf1 and ccr4p (44 kDa, Protein from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna, rna (Complex from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Spt4,spt5, paf1p,spt16,pob3 (Complex from Komagataella phaffii)
- Spt6 (Complex from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Protein that interacts with spt6p and copurifies with spt5p and rna polymerase ii (46 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Component of the paf1p complex (124 kDa, Protein from Komagataella phaffii)
- Fact complex subunit (115 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Transcription elongation factor spt6 (173 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii elongation complex transcribing a nucleosome (ec49b) (Complex)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rnapii-associated chromatin remodeling paf1 complex subunit (62 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rnap ii-associated protein (46 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*ap*cp*cp*cp*gp*gp*gp*up*gp*up*cp*up*up*cp*cp*cp*cp*a)-3') (6 kDa, RNA from synthetic construct)
- Fact complex subunit pob3 (60 kDa, Protein from Komagataella phaffii)