ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
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 ]
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (Protein)
- Histone h2a (Protein from Xenopus laevis)
- Ubiquitin (Protein)
- Dna (309-mer) (DNA from synthetic construct)
- Polycomb complex protein bmi-1 (Protein)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Protein)
- Histone h3.2 (Protein from Xenopus laevis)
Resolution: 8.8 Å
EM Method: Single-particle
Fitted PDBs: 7vvz
Q-score: 0.108
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nua4 bound to the nucleosome (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- Epl1 arginine anchor (1 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae S288C)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 6x0n
Q-score: 0.113
Bilokapic S, Suskiewicz MJ, Ahel I, Halic M
Nature (2020) 585 pp. 609-613 [ DOI: doi:10.1038/s41586-020-2725-7 Pubmed: 32939087 ]
- Dna (Complex from synthetic construct)
- Histone parylation factor 1 (40 kDa, Protein from Homo sapiens)
- Poly [adp-ribose] polymerase 2 (67 kDa, Protein from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from African clawed frog)
- Histone parylation factor 1, poly [adp-ribose] polymerase 2 (Complex from Homo sapiens)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1, histone parylation factor 1, poly [adp-ribose] polymerase 2/dna complex (100 kDa, Complex)
SWI/SNF nucleosome complex with ADP-BeFx
Resolution: 8.96 Å
EM Method: Single-particle
Fitted PDBs: 6uxw
Q-score: 0.122
Han Y, Reyes AA, Malik S, He Y
Nature (2020) 579 pp. 452-455 [ DOI: doi:10.1038/s41586-020-2087-1 Pubmed: 32188938 ]
- Swi/snf global transcription activator complex subunit swp82 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swi/snf nucleosome complex with adp-befx (Complex from Saccharomyces cerevisiae)
- 601 sequence top strand (61 kDa, DNA from synthetic construct)
- Swi/snf chromatin-remodeling complex subunit swi1 (148 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf6 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf chromatin-remodeling complex subunit snf5 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Water (18 Da, Ligand)
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription regulatory protein snf12 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Phosphate ion (94 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf2 (194 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf complex subunit swi3 (93 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 sequence bottom strand (56 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))