SNF2H bound to nucleosome - Class E1
Malik D, Deshmukh A, Bilokapic S, Halic M
bioRxiv (2025) [ Pubmed: 39803580 DOI: doi:10.1101/2024.12.31.630910 ]
- Histone h4 (Protein from Xenopus laevis)
- Snf2h bound to nucleosome - class e2 (Complex from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (Protein)
- Dna(150-mer) (DNA from synthetic construct)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- Dna(149-mer) (DNA from synthetic construct)
- Histone h3 (Protein from Xenopus laevis)
Map focused on RYBP/Ub of 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 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (309-mer) (Complex from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
Map focused on RING1B/BMI1 of 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 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (309-mer) (Complex from synthetic construct)
- Ubiquitin (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 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Prc2 monomer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
- 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)
- Prc2 (Complex from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Prc2-j119-450 monomer bound to h1-nucleosome (290 kDa, Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Nucleosome (Complex from Xenopus laevis)
- Histone h1.0 (21 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 9gd1
Q-score: 0.332
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ Pubmed: 39270644 DOI: doi:10.1016/j.molcel.2024.08.022 ]
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (261-mer) (81 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp.
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 9gd2
Q-score: 0.295
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ Pubmed: 39270644 DOI: doi:10.1016/j.molcel.2024.08.022 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (248-mer) (77 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. (Complex from Xenopus laevis)
- Dna (248-mer) (76 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7yrg
Q-score: 0.227
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z
Mol Cell (2023) 83 pp. 2884-2895.e7 [ Pubmed: 37536340 DOI: doi:10.1016/j.molcel.2023.07.001 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (12 kDa, Protein from Xenopus laevis)
- Histone,suv420h1 (Complex from Xenopus laevis)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (146-mer) (45 kDa, DNA from Homo sapiens)
- [histone h4]-n-methyl-l-lysine20 n-methyltransferase kmt5b (32 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Histone methyltransferase and nucleosome complex (Complex)
- Histone (Complex from Homo sapiens)
structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8cbq
Q-score: 0.304
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Dna (Complex from Homo sapiens)
- Ledgf/p75 pwwp domain complex (Complex)
- H3k36me3 dinucleosome-ledgf/p75 pwwp domain complex (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Histone (Complex from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (50 kDa, DNA from synthetic construct)
Cryo-EM structure of an asymmetric nucleosome (10-N-0) from a Glacios/Falcon3EC
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S
eLife (2021) 10 [ Pubmed: 34486521 DOI: doi:10.7554/eLife.71420 ]
- Histone h4 (Protein from Xenopus laevis)
- Histone h2a type 1 (Protein from Xenopus laevis)
- 601 nucleosome with 10 additional bp (205 kDa, Complex)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Widom 601 sequence with 10 additional bp on the strong side (DNA from synthetic construct)