Cryo-EM structure of native H2AK119bu nucleosome at 2.6
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8vlr
Q-score: 0.602
Shen XY, Chen CX, Wang Y, Zheng W, Zheng JH, Jones AE, Zhu B, Zhang H, Lyons C, Rijal A, Moley JA, Cao GS, Liu K, Winn R, McGinty RK, Zhang K, Wang HB
To Be Published
- Native h2ak119bu nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (136-mer) (41 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-a (10 kDa, Protein from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Dna (136-mer) (42 kDa, DNA from Homo sapiens)
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 h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- 601 i strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Nucleosome containing 8oxog at shl-6 (Complex from Homo sapiens)
- 601 j strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 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 h2a type 1 (13 kDa, Protein from Homo sapiens)
- N-glycosylase/dna lyase (38 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- 601 i strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 j strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ogg1 bound to a nucleosome containing 8oxog at shl-6 (composite map) (Complex 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 ]
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosome containing 8oxog at shl4 (Complex 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 ]
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- N-glycosylase/dna lyase (38 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 h3.2 (15 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ogg1 bound to a nucleosome containing 8oxog at shl4 (composite map) (Complex 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 ]
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
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 ]
- Histone h2ak119c (Protein 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)
- Histone h4 (Protein from Homo sapiens)
- Histone h3 (Protein from Homo sapiens)
- Dnmt3a1 (Protein from Homo sapiens)
- Dnmt3l (Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- 195bp widom601 dna (DNA from synthetic construct)
- Ubiquitin (Protein from Homo sapiens)
- Histone h2b (Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- E1a-binding protein p400 (343 kDa, Protein from Homo sapiens)
- Enhancer of polycomb homolog 1 (93 kDa, Protein from Homo sapiens)
- Reconstituted p400 subcomplex of the human tip60 complex (Complex from Homo sapiens)
- Histone h2b type 1-b (13 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
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 [ Pubmed: 37427792 DOI: doi:10.1093/nar/gkad577 ]
- Histone octamer (Complex from Trypanosoma brucei brucei TREU927)
- Histone h2b (12 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Histone h3, putative (14 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Widom 601 145 bp dna (127-mer ordered and built) (44 kDa, DNA from synthetic construct)
- Nucleosome core particle (89 kDa, Complex 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 h4 (11 kDa, Protein from Trypanosoma brucei brucei TREU927)
- Widom 601 145 bp dna (127-mer ordered and built) (44 kDa, DNA from synthetic construct)
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)
- Histone h1.0-b (Complex from Xenopus laevis)
- 197-bp h1-bound palindromic nucleosome (120 kDa, Complex from Homo sapiens)