Cryo-EM structure of the overlapping di-nucleosome (closed form)
Shimizu M, Tanaka H, Nishimura M, Sato N, Nozawa K, Ehara H, Sekine SI, Morishima K, Inoue R, Takizawa Y, Kurumizaka H, Sugiyama M
Pnas Nexus (2024) 3 pp. pgae484-pgae484 [ DOI: doi:10.1093/pnasnexus/pgae484 Pubmed: 39539301 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex from Homo sapiens)
Cryo-EM structure of the overlapping di-nucleosome (intermediate form2)
Shimizu M, Tanaka H, Nishimura M, Sato N, Nozawa K, Ehara H, Sekine SI, Morishima K, Inoue R, Takizawa Y, Kurumizaka H, Sugiyama M
Pnas Nexus (2024) 3 pp. pgae484-pgae484 [ DOI: doi:10.1093/pnasnexus/pgae484 Pubmed: 39539301 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex from Homo sapiens)
Cryo-EM structure of the overlapping di-nucleosome (open form)
Shimizu M, Tanaka H, Nishimura M, Sato N, Nozawa K, Ehara H, Sekine SI, Morishima K, Inoue R, Takizawa Y, Kurumizaka H, Sugiyama M
Pnas Nexus (2024) 3 pp. pgae484-pgae484 [ DOI: doi:10.1093/pnasnexus/pgae484 Pubmed: 39539301 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex 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 ]
- 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)
Structure of human Sox2 transcription factor in complex with a nucleosome
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 6t7b
Q-score: 0.217
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P
Nature (2020) 580 pp. 669-672 [ DOI: doi:10.1038/s41586-020-2195-y Pubmed: 32350470 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1, h2b type 1-k, h3.2, h4 and sox2 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (10 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Structure of human sox2 transcription factor in complex with a nucleosome (Complex)
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA
Resolution: 5.6 Å
EM Method: Single-particle
Fitted PDBs: 6a5l
Q-score: 0.182
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (Complex from Komagataella phaffii)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Cryo-EM structure of CENP-A nucleosome complexed with CENP-LN
Tian T, Li X, Liu Y, Wang C, Liu X, Bi G, Zhang X, Yao X, Zhou ZH, Zang J
Cell Res (2018) 28 pp. 374-378 [ Pubmed: 29350209 DOI: doi:10.1038/cr.2018.13 ]
- Cenp-nl complex (Complex)
- Cenp-a ncp (Complex)
- Cenp-a ncp/cenp-ln complex (Complex from Homo sapiens)
- Histone h2a (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Dna (147-mer) (DNA from Homo sapiens)
- Histone h3-like centromeric protein a (cenp-a) (Protein from Homo sapiens)
- Histone h2b (Protein from Homo sapiens)
- Centromere protein l (cenp-l) (Protein from Homo sapiens)
- Centromere protein n (cenp-n) (Protein from Homo sapiens)
Nucleosome breathing : Class 2
Resolution: 5.4 Å
EM Method: Single-particle
Fitted PDBs: 6esg
Q-score: 0.198
Bilokapic S, Strauss M, Halic M
Nat Struct Mol Biol (2018) 25 pp. 101-108 [ DOI: doi:10.1038/s41594-017-0005-5 Pubmed: 29323273 ]
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (141-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from Synthetic construct)
- Dna (141-mer) (45 kDa, DNA from synthetic construct)
- Nucleosome (200 kDa, Complex)
Nucleosome breathing : Class 3
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 6esh
Q-score: 0.209
Bilokapic S, Strauss M, Halic M
Nat Struct Mol Biol (2018) 25 pp. 101-108 [ DOI: doi:10.1038/s41594-017-0005-5 Pubmed: 29323273 ]
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Nucleosome (200 kDa, Complex)
- Nucleosome (Complex from Xenopus laevis)