Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eoz
Q-score: 0.465
Ren M, Gut F, Fan Y, Ma J, Shan X, Yikilmazsoy A, Likhodeeva M, Hopfner KP, Zhou C
Nat Commun (2024) 15 pp. 9407-9407 [ DOI: doi:10.1038/s41467-024-53811-3 Pubmed: 39477986 ]
- Widom 601 dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Widom 601 dna (145-mer) (45 kDa, DNA from synthetic construct)
- Nucleosome core particle (Complex from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (Complex from synthetic construct)
- Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle (Complex)
- N-glycosylase/dna lyase (40 kDa, Protein from Homo sapiens)
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
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)
H2BK120ub-modified nucleosome ubiquitin position 1
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8v25
Q-score: 0.519
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H2BK120ub-modified nucleosome ubiquitin position 2
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8v26
Q-score: 0.515
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H2BK120ub-modified nucleosome ubiquitin position 3
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8v27
Q-score: 0.516
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H2BK120ub-modified nucleosome ubiquitin position 4
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8v28
Q-score: 0.505
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8ybj
Q-score: 0.631
Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H
Genes Cells (2024) 29 pp. 769-781 [ Pubmed: 38972377 DOI: doi:10.1111/gtc.13143 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- The human nucleosome containing h3.1 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)