Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8skz
Q-score: 0.458
To Be Published
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (192-mer) (59 kDa, DNA from Homo sapiens)
- Dna (192-mer) (59 kDa, DNA from Homo sapiens)
- Cryo-em complex of ddm1-hells chimera bound to the nucleosome (Complex from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (12 kDa, Protein from Xenopus laevis)
- Atp-dependent dna helicase ddm1,lymphoid-specific helicase chimera (93 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
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 ]
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
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)
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9dg3
Q-score: 0.382
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 ]
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
ncPRC1RYBP bound to unmodified nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 9dgg
Q-score: 0.47
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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Nucleosome core particle containing an 8-oxoG damage site
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vx5
Q-score: 0.493
You Q, Feng X, Cai Y, Baylin SB, Li H
Commun Biol (2024) 7 pp. 1202-1202 [ Pubmed: 39341999 DOI: doi:10.1038/s42003-024-06919-7 ]
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Complex of human ogg1 with a 35 bp dna duplex containing 8-oxog (Complex from Homo sapiens)
- Histone h2a (18 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Human OGG1 bound at the nucleosomal DNA entry site
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8vx6
Q-score: 0.424
You Q, Feng X, Cai Y, Baylin SB, Li H
Commun Biol (2024) 7 pp. 1202-1202 [ Pubmed: 39341999 DOI: doi:10.1038/s42003-024-06919-7 ]
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- N-glycosylase/dna lyase (43 kDa, Protein from Homo sapiens)
- Histone h2a (18 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Complex of human ogg1 with a 35 bp dna duplex containing 8-oxog (Complex from Homo sapiens)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
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 ]
- Automethylated prc2 dimer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- 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)
- Proximal prc2 (Complex from Homo sapiens)
- Distal prc2 (Complex from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Activating methylated peptide (1 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 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 [ 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)