Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8siy
Q-score: 0.497
Sahu S, Ekundayo BE, Kumar A, Bleichert F
EMBO J (2023) 42 pp. e114654-e114654 [ DOI: doi:10.15252/embj.2023114654 Pubmed: 37551430 ]
- Leucine-rich repeat and wd repeat-containing protein 1 (71 kDa, Protein from Rattus norvegicus)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2, histone h4, histone h2a, histone h2b, widom 601 dna (Complex from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Origin recognition complex subunit 2 (11 kDa, Protein from Rattus norvegicus)
- Leucine-rich repeat and wd repeat-containing protein 1, origin recognition complex subunit 2 (Complex from Rattus norvegicus)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Orca-nucleosome (h4k20me3) complex (Complex)
- Widom 601 dna (47 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Widom 601 dna (46 kDa, DNA from synthetic construct)
Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ssa
Q-score: 0.449
Donovan BT, Chen H, Eek P, Meng Z, Jipa C, Tan S, Bai L, Poirier MG
Mol Cell (2023) 83 pp. 1251-1263.e6 [ Pubmed: 36996811 DOI: doi:10.1016/j.molcel.2023.03.006 ]
- Histone h2a.1 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (137-mer) (46 kDa, DNA from synthetic construct)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1, histone h2b.1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Centromere-binding protein 1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pioneer factor cbf1 in complex with the nucleosome (286 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3.2, histone h4 (Complex from Xenopus laevis)
- Centromere-binding protein 1 (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
Structure of VRK1 C-terminal tail bound to nucleosome core particle
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7tan
Q-score: 0.56
Budziszewski GR, Zhao Y, Spangler CJ, Kedziora KM, Williams MR, Azzam DN, Skrajna A, Koyama Y, Cesmat AP, Simmons HC, Arteaga EC, Strauss JD, Kireev D, McGinty RK
Nucleic Acids Res (2022) 50 pp. 4355-4371 [ DOI: doi:10.1093/nar/gkac198 Pubmed: 35390161 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Structure of vrk1 c-terminal tail bound to nucleosome core particle (Complex)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Widom 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b type 1-c/e/f/g/i, serine/threonine-protein kinase vrk1 (Complex from Homo sapiens)
- Serine/threonine-protein kinase vrk1 (45 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
Uncrosslinked VRK1-nucleosome complex
Budziszewski GR, Zhao Y, Spangler CJ, Kedziora KM, Williams MR, Azzam DN, Skrajna A, Koyama Y, Cesmat AP, Simmons HC, Arteaga EC, Strauss JD, Kireev D, McGinty RK
Nucleic Acids Res (2022) 50 pp. 4355-4371 [ DOI: doi:10.1093/nar/gkac198 Pubmed: 35390161 ]
- Structure of vrk1 c-terminal tail bound to nucleosome core particle (Complex)
- Widom 601 dna (185-mer) (DNA from synthetic construct)
- Histone h3.2 (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Vaccinia-related kinase 1 (Protein from Homo sapiens)
- Histone h2a (Protein from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b type 1-c/e/f/g/i, serine/threonine-protein kinase vrk1 (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2b (Protein from Homo sapiens)
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6w5i
Q-score: 0.135
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6w5m
Q-score: 0.177
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 6w5n
Q-score: 0.167
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Bilokapic S, Suskiewicz MJ, Ahel I, Halic M
Nature (2020) 585 pp. 609-613 [ Pubmed: 32939087 DOI: doi:10.1038/s41586-020-2725-7 ]
- Histone parylation factor 1, poly [adp-ribose] polymerase 2 (Complex from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1, histone parylation factor 1, poly [adp-ribose] polymerase 2/dna complex (100 kDa, Complex)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from African clawed frog)
- Dna (Complex from synthetic construct)
Bilokapic S, Suskiewicz MJ, Ahel I, Halic M
Nature (2020) 585 pp. 609-613 [ Pubmed: 32939087 DOI: doi:10.1038/s41586-020-2725-7 ]
- Histone parylation factor 1, poly [adp-ribose] polymerase 2 (Complex from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1, histone parylation factor 1, poly [adp-ribose] polymerase 2/dna complex (100 kDa, Complex)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from African clawed frog)
- Dna (Complex from synthetic construct)
Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 6wz5
Q-score: 0.504
Bilokapic S, Suskiewicz MJ, Ahel I, Halic M
Nature (2020) 585 pp. 609-613 [ Pubmed: 32939087 DOI: doi:10.1038/s41586-020-2725-7 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1/dna complex 2 (240 kDa, Complex)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Dna (153-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Dna (153-mer) (51 kDa, DNA from synthetic construct)