Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8rup
Q-score: 0.551
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9b3i
Q-score: 0.293
Fung HYJ, Jiou J, Niesman AB, Bernardes NE, Chook YM
J Cell Biol (2025) 224 [ DOI: doi:10.1083/jcb.202408193 Pubmed: 39601790 ]
- Nap1 isoform 1 (48 kDa, Protein from Saccharomyces cerevisiae)
- Gtp-binding nuclear protein (21 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Kap114 isoform 1 (114 kDa, Protein from Saccharomyces cerevisiae)
- Complex of kap114 bound to ran gtpase gsp1, h2a-h2b and nap1 (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Histone h2b (14 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9b1e
Q-score: 0.191
Louder RK, Park G, Ye Z, Cha JS, Gardner AM, Lei Q, Ranjan A, Hollmuller E, Stengel F, Pugh BF, Wu C
Cell (2024) 187 pp. 6849-6864.e18 [ DOI: doi:10.1016/j.cell.2024.09.007 Pubmed: 39357520 ]
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- Dna (214-mer) (65 kDa, DNA from synthetic construct)
- Swr1-complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Native swr1 bound to nucleosome. (1 MDa, Complex from Saccharomyces cerevisiae)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae W303)
- Helicase swr1 (178 kDa, Protein from Saccharomyces cerevisiae W303)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- Histone h2b (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Saccharomyces cerevisiae)
- Native swr1 complex (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Drosophila melanogaster)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Ruvb-like protein 1 (91 kDa, Protein from Saccharomyces cerevisiae W303)
- Dna (214-mer) (66 kDa, DNA from synthetic construct)
SWR1-nucleosome complex in configuration 1
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qku
Q-score: 0.363
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ DOI: doi:10.1038/s41586-024-08152-y Pubmed: 39506114 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
SWR1-nucleosome complex in configuration 2
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 8qkv
Q-score: 0.185
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ DOI: doi:10.1038/s41586-024-08152-y Pubmed: 39506114 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (194-mer) (60 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (194-mer) (59 kDa, DNA from synthetic construct)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qz0
Q-score: 0.293
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ Pubmed: 39226902 DOI: doi:10.1016/j.molcel.2024.08.015 ]
- Dna (113-mer) (36 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (113-mer) (36 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a.z (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.z-specific chaperone chz1 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-hexasome-dimer complex (Complex from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Swr1-complex protein 5 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9ipu
Q-score: 0.237
Shi Q, Deng ZH, Zhang LY, Tong ZB, Chu G-C, Ai HS, Liu L
To Be Published
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (22 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (171-mer) (52 kDa, DNA from Homo sapiens)
- Dna (171-mer) (52 kDa, DNA from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Cryo-em structure of the rnf168(1-193)/ubch5c-ub ubiquitylation module bound to h1.0-k63-ub3 modified chromatosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h1.0 (20 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
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 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]
- Proximal prc2 (Complex from Homo sapiens)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Distal prc2 (Complex from Homo sapiens)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Activating methylated peptide (1 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Automethylated prc2 dimer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
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 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Prc2 monomer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Prc2 (Complex from Homo sapiens)
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 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]
- Protein jumonji (36 kDa, Protein from Homo sapiens)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Histone h1.0 (21 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Prc2-j119-450 monomer bound to h1-nucleosome (290 kDa, Complex from Homo sapiens)
- Prc2 (Complex from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)