H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vo0
Q-score: 0.258
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01452-x Pubmed: 39774834 ]
- Histone h4 (8 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (9 kDa, Protein from Xenopus laevis)
- Histone h4 (8 kDa, Protein from Homo sapiens)
- H3k36me3 modified nucleosome core particle (Complex from Homo sapiens)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (9 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
H3K36me3-modified nucleosome bound to PRC2_AJ1-450
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vob
Q-score: 0.375
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01452-x Pubmed: 39774834 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
- H3k36me3 nucleosome core particle bound to prc2_aj1-450 (Complex from Homo sapiens)
- Dna (157-mer) (48 kDa, DNA from Homo sapiens)
- Histone h2a type 1 (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of ISW1a-dinucleosome
Resolution: 5.4 Å
EM Method: Single-particle
Fitted PDBs: 7x3t
Q-score: 0.192
Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z
Nat Struct Mol Biol (2024) 31 pp. 266-274 [ Pubmed: 38177688 DOI: doi:10.1038/s41594-023-01174-6 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Iswi one complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae S288C)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Dna (343-mer) (108 kDa, DNA from synthetic construct)
- Isw1a-dinucleosome (392 MDa, Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna(343-mer) (109 kDa, DNA from synthetic construct)
Cryo-EM structure of IOC3-N2 nucleosome
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7x3v
Q-score: 0.502
Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z
Nat Struct Mol Biol (2024) 31 pp. 266-274 [ DOI: doi:10.1038/s41594-023-01174-6 Pubmed: 38177688 ]
- N2 nucleosome (Complex)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ioc3 (Complex)
- Iswi one complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (Complex from Saccharomyces cerevisiae S288c)
- Ioc3-n2 nucleosome (392 MDa, Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of ISW1-N1 nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7x3w
Q-score: 0.489
Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z
Nat Struct Mol Biol (2024) 31 pp. 266-274 [ DOI: doi:10.1038/s41594-023-01174-6 Pubmed: 38177688 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ioc3 (Complex)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ioc3-n2 nucleosome (392 MDa, Complex from Xenopus laevis)
- Dna (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- N2 nucleosome (Complex from Saccharomyces cerevisiae S288c)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of N1 nucleosome-RA
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7x3x
Q-score: 0.44
Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z
Nat Struct Mol Biol (2024) 31 pp. 266-274 [ DOI: doi:10.1038/s41594-023-01174-6 Pubmed: 38177688 ]
- N2 nucleosome (Complex)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ioc3 (Complex)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ioc3-n2 nucleosome (392 MDa, Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from Saccharomyces cerevisiae S288C)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7zs9
Q-score: 0.34
Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 226-232 [ Pubmed: 36411341 DOI: doi:10.1038/s41594-022-00865-w ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Non-template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with the +1 nucleosome (1 MDa, Complex from Saccharomyces killer virus M2-4)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7zsa
Q-score: 0.342
Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 226-232 [ DOI: doi:10.1038/s41594-022-00865-w Pubmed: 36411341 ]
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp (1 MDa, Complex from Saccharomyces cerevisiae)
- Non-template dna (209-mer) (64 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7zsb
Q-score: 0.277
Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 226-232 [ Pubmed: 36411341 DOI: doi:10.1038/s41594-022-00865-w ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Template dna (219-mer) (67 kDa, DNA from synthetic construct)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Non-template dna (219-mer) (67 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii-spt4/5-chd1-nucleosome (Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- 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 rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (116 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Chromatin elongation factor spt4 (11 kDa, Protein 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 rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Rna (21 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (139-mer) (56 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (128-mer) (54 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)