Nucleosome containing 8oxoG at SHL-6
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vws
Q-score: 0.534
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ Pubmed: 39715760 DOI: doi:10.1038/s41467-024-55497-z ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- 601 j strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Nucleosome containing 8oxog at shl-6 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vwt
Q-score: 0.41
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ Pubmed: 39715760 DOI: doi:10.1038/s41467-024-55497-z ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Ogg1 bound to a nucleosome containing 8oxog at shl-6 (composite map) (Complex from Homo sapiens)
- 601 j strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- N-glycosylase/dna lyase (38 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
Nucleosome containing 8oxoG at SHL4
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8vwu
Q-score: 0.559
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ Pubmed: 39715760 DOI: doi:10.1038/s41467-024-55497-z ]
- 601 i strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Nucleosome containing 8oxog at shl4 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- 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)
OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8vwv
Q-score: 0.359
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA
Nat Commun (2024) 15 pp. 10722-10722 [ Pubmed: 39715760 DOI: doi:10.1038/s41467-024-55497-z ]
- 601 i strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Ogg1 bound to a nucleosome containing 8oxog at shl4 (composite map) (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- N-glycosylase/dna lyase (38 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 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)
Cryo-EM density map of DNMT3A1-DNMT3L on a human H2AKc119ub nucleosome at 5.1 A resolution
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 ]
- Dnmt3a1 (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- 195bp widom601 dna (DNA from synthetic construct)
- Histone h2ak119c (Protein from Homo sapiens)
- Dnmt3l (Protein from Homo sapiens)
- Histone h3 (Protein from Homo sapiens)
- Ubiquitin (Protein from Homo sapiens)
- Histone h2b (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)
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)
H1-bound palindromic nucleosome, state 4
Louro JA, Boopathi R, Beinsteiner B, Mohideen Patel AK, Cheng TC, Angelov D, Hamiche A, Bendar J, Kale S, Klaholz BP, Dimitrov S
Structure (2023) 31 pp. 201-212.e5 [ DOI: doi:10.1016/j.str.2022.12.005 Pubmed: 36610392 ]
- Core histone octamer (Complex)
- 197-bp h1-bound palindromic nucleosome (120 kDa, Complex from Homo sapiens)
- Histone h1.0-b (Complex from Xenopus laevis)
H1-bound palindromic nucleosome, state 3
Louro JA, Boopathi R, Beinsteiner B, Mohideen Patel AK, Cheng TC, Angelov D, Hamiche A, Bendar J, Kale S, Klaholz BP, Dimitrov S
Structure (2022) [ DOI: doi:10.1016/j.str.2022.12.005 Pubmed: 36610392 ]
- Core histone octamer (Complex)
- Dna (Complex from Homo sapiens)
- 197-bp h1-bound palindromic nucleosome (120 kDa, Complex from Homo sapiens)
- Histone h1.0-b (Complex from Xenopus laevis)
H1-bound palindromic nucleosome, state 2
Louro JA, Boopathi R, Beinsteiner B, Mohideen Patel AK, Cheng TC, Angelov D, Hamiche A, Bendar J, Kale S, Klaholz BP, Dimitrov S
Structure (2023) 31 pp. 201-212.e5 [ DOI: doi:10.1016/j.str.2022.12.005 Pubmed: 36610392 ]
- Core histone octamer (Complex)
- 197-bp h1-bound palindromic nucleosome (120 kDa, Complex from Homo sapiens)
- Histone h1.0-b (Complex from Xenopus laevis)