ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dde
Q-score: 0.456
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h1.4 (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8vg2
Q-score: 0.493
Mol Cell (2024) [ ]
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Foxa1 and gata4 in complex with h1.4 chromatosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (196-mer) (65 kDa, DNA from synthetic construct)
- Dna (196-mer) (64 kDa, DNA from synthetic construct)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h1.4 (22 kDa, Protein from Homo sapiens)
Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8h1t
Q-score: 0.435
Ge W, Yu C, Li J, Yu Z, Li X, Zhang Y, Liu CP, Li Y, Tian C, Zhang X, Li G, Zhu B, Xu RM
Nature (2023) 616 pp. 176-182 [ DOI: doi:10.1038/s41586-023-05841-y Pubmed: 36991118 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cryo-em structure of bap1-asxl1 bound to chromatosome (Complex from Homo sapiens)
- Dna (187-mer) (58 kDa, DNA from Homo sapiens)
- Histone h2a type 1-d (14 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h1.4 (23 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from Homo sapiens)
- Polycomb group protein asxl1 (41 kDa, Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
The 4x177 nucleosome array containing H1
Resolution: 9.5 Å
EM Method: Single-particle
Fitted PDBs: 7pet
Q-score: 0.105
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Tetranucleosome from 4x177 nucleosome array (Complex)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (702-mer) (218 kDa, DNA from synthetic construct)
- Dna (702-mer) (215 kDa, DNA from synthetic construct)
Trinucleosome of the 4x177 nucleosome array containing H1
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 7peu
Q-score: 0.138
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ Pubmed: 35581345 DOI: doi:10.1038/s41594-022-00768-w ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (522-mer) (161 kDa, DNA from synthetic construct)
- Trinucleosome from 4x177 nucleosome array (Complex)
- Dna (522-mer) (160 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Nucleosome 2 of the 4x177 nucleosome array containing H1
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7pex
Q-score: 0.267
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ Pubmed: 35581345 DOI: doi:10.1038/s41594-022-00768-w ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Nucleosome 2 from 4x177 nucleosome array (Complex)
- Dna (177-mer) (55 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Nucleosome 4 of the 4x177 nucleosome array containing H1
Resolution: 7.9 Å
EM Method: Single-particle
Fitted PDBs: 7pez
Q-score: 0.203
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (182-mer) (55 kDa, DNA from synthetic construct)
- Dna (182-mer) (56 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Nucleosome 4 from 4x177 nucleosome array (Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
Trinucleosome of the 4x177 nucleosome array containing H1
Resolution: 11.0 Å
EM Method: Single-particle
Fitted PDBs: 7pf0
Q-score: 0.101
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna (563-mer) (166 kDa, DNA from synthetic construct)
- Dna (563-mer) (167 kDa, DNA from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Trinucleosome from 4x187 nucleosome array (Complex)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
Nucleosome stack of the 4x187 nucleosome array containing H1
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7pf2
Q-score: 0.217
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Dna (541-mer) (230 kDa, DNA from synthetic construct)
- Dna (541-mer) (232 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Nucleosome stack from 4x187 nucleosome array (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
Nucleosome 4 of the 4x187 nucleosome array containing H1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7pf3
Q-score: 0.351
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ Pubmed: 35581345 DOI: doi:10.1038/s41594-022-00768-w ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Nucleosome 4 from 4x187 nucleosome array (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)