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)
Structure of the Nucleosome Core Particle from Trypanosoma brucei
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8com
Q-score: 0.439
Deak G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson JA, Tuijtel MW, Webb S, Wilson MD
Nucleic Acids Res (2023) 51 pp. 7882-7899 [ DOI: doi:10.1093/nar/gkad577 Pubmed: 37427792 ]
- Histone octamer (Complex from Trypanosoma brucei brucei TREU927)
- Nucleosome core particle (89 kDa, Complex from Trypanosoma brucei brucei TREU927)
- Histone h2b (12 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Widom 601 145 bp dna (127-mer ordered and built) (44 kDa, DNA from synthetic construct)
- Widom 601 145 bp dna (127-mer ordered and built) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Histone h2a (14 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Widom 601 145 bp dna (Complex from synthetic construct)
- Histone h3, putative (14 kDa, Protein from Trypanosoma brucei brucei TREU927)