Automethylated PRC2 dimer bound to nucleosome
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 8t9g
Q-score: 0.163
Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S
Mol Cell (2024) 84 pp. 3885-3898.e8 [ DOI: doi:10.1016/j.molcel.2024.08.025 Pubmed: 39303719 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Activating methylated peptide (1 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
- Automethylated prc2 dimer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Proximal prc2 (Complex from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Distal prc2 (Complex from Homo sapiens)
PRC2 monomer bound to nucleosome
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8tas
Q-score: 0.259
Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S
Mol Cell (2024) 84 pp. 3885-3898.e8 [ DOI: doi:10.1016/j.molcel.2024.08.025 Pubmed: 39303719 ]
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Prc2 monomer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Prc2 (Complex from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
PRC2-J119-450 monomer bound to H1-nucleosome
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8tb9
Q-score: 0.261
Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S
Mol Cell (2024) 84 pp. 3885-3898.e8 [ DOI: doi:10.1016/j.molcel.2024.08.025 Pubmed: 39303719 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h1.0 (21 kDa, Protein from Homo sapiens)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Prc2-j119-450 monomer bound to h1-nucleosome (290 kDa, Complex from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Protein jumonji (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Prc2 (Complex from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
P400 subcomplex of the native human TIP60 complex
Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Cote J, Nogales E
Science (2024) 385 pp. eadl5816-eadl5816 [ Pubmed: 39088653 DOI: doi:10.1126/science.adl5816 ]
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Reconstituted p400 subcomplex of the human tip60 complex (Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- E1a-binding protein p400 (343 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Histone h2b type 1-b (13 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Enhancer of polycomb homolog 1 (93 kDa, Protein from Homo sapiens)
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7i
Q-score: 0.443
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8x7j
Q-score: 0.391
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes complex determined by activity-based chemical trapping strategy (Complex from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7k
Q-score: 0.423
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (143-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Cryo-em structures of rnf168/ubch5c-ub in complex with h2ak13ub nucleosomes determined by activity-based chemical trapping strategy (adjacent h2ak13/15 dual-monoubiquitination) (Complex from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
Structure of human APC3loop 375-381 bound to the NCP
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9fgq
Q-score: 0.651
Cirillo L, Young R, Veerapathiran S, Roberti A, Martin M, Abubacar A, Perosa C, Coates C, Muhammad R, Roumeliotis TI, Choudhary JS, Alfieri C, Pines J
EMBO J (2024) 43 pp. 4324-4355 [ Pubmed: 39143240 DOI: doi:10.1038/s44318-024-00194-2 ]
- Histone h2a type 2-a (14 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-b (29 kDa, Protein from Homo sapiens)
- Dna (132-mer) (64 kDa, DNA from Homo sapiens)
- Cell division cycle protein 27 homolog (32 kDa, Protein from Homo sapiens)
- Dna (131-mer) (65 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Apc3 motif bound to the ncp acidic patch (Complex from Homo sapiens)
Structure of CyclinB1 N-terminus bound to the NCP
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9fh9
Q-score: 0.534
Cirillo L, Young R, Veerapathiran S, Roberti A, Martin M, Abubacar A, Perosa C, Coates C, Muhammad R, Roumeliotis TI, Choudhary JS, Alfieri C, Pines J
EMBO J (2024) 43 pp. 4324-4355 [ Pubmed: 39143240 DOI: doi:10.1038/s44318-024-00194-2 ]
- Water (18 Da, Ligand)
- G2/mitotic-specific cyclin-b1 (2 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 3 (14 kDa, Protein from Homo sapiens)
- Dna (145-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Cyclin b1 ntd bound to the acidic path of the ncp (Complex from Homo sapiens)
human RYBP-PRC1 bound to H2AK118ub1 nucleosome
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8pp6
Q-score: 0.465
Ciapponi M, Karlukova E, Schkolziger S, Benda C, Muller J
Nat Struct Mol Biol (2024) 31 pp. 1023-1027 [ DOI: doi:10.1038/s41594-024-01258-x Pubmed: 38528151 ]
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Human rybp-prc1 bound to h2ak118ub1 nucleosome (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (25 kDa, Protein from Homo sapiens)
- Drosophila octamer (Complex from Drosophila melanogaster)
- Dna (Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Human rybp (Complex from Homo sapiens)
- Histone h2a (13 kDa, Protein from Drosophila melanogaster)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Human ubiquitin (Complex from Homo sapiens)
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Histone h3 (fragment) (15 kDa, Protein from Drosophila melanogaster)
- Ubiquitin-40s ribosomal protein s27a (fragment) (8 kDa, Protein from Homo sapiens)