Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7e9c
Q-score: 0.311
Jiang H, Yu C, Liu CP, Han X, Yu Z, Xu RM
To Be Published
- Dna (147-mer) (45 kDa, DNA from Escherichia coli)
- Origin recognition complex subunit 1 (Complex)
- Histone h2a.2 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from Escherichia coli)
- Histone h2b.2 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (147-mer) (45 kDa, DNA from Escherichia coli)
- Histone (Complex from Saccharomyces cerevisiae)
- Yeast orc1 bah domain in complex with 147-bp nucleosome (Complex from Saccharomyces cerevisiae)
- Origin recognition complex subunit 1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ Pubmed: 33479126 DOI: doi:10.1126/science.abc6663 ]
- Histone h3.2 (Protein from Xenopus lenduensis)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Dna (146-mer) (Complex from Synthetic)
- Dna (146-mer) (DNA from synthetic construct)
- Noncatalytic conformation dot1 bound to the unacetylated h4 nucleosome (Complex from Saccharomyces cerevisiae)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Saccharomyces cerevisiae)
- Polyubiquitin-b (Protein from Homo sapiens)
- Polyubiquitin-b (Complex from Homo sap)
Active state Dot1 bound to the H4K16ac nucleosome, Ubiquitin focused map
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ Pubmed: 33479126 DOI: doi:10.1126/science.abc6663 ]
- Histone h2a type 1 (Protein from Xenopus laevis)
- Dna (146-mer) (Complex from Synthetic)
- Polyubiquitin-b (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Active state dot1 bound to the h4k16 acetylated nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h4 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Xenopus laevis)
- Dna (146-mer) (DNA from synthetic construct)
- Polyubiquitin-b (Complex from Homo sap)
Active state Dot1 bound to the unacetylated H4 nucleosome, Ubiquitin focused map
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ Pubmed: 33479126 DOI: doi:10.1126/science.abc6663 ]
- Histone h2a type 1 (Protein from Xenopus laevis)
- Dna (146-mer) (Complex from Synthetic)
- Active state dot1 bound to the unacetylated h4 nucleosome (Complex from Saccharomyces cerevisiae)
- Polyubiquitin-b (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Xenopus laevis)
- Dna (146-mer) (DNA from synthetic construct)
- Polyubiquitin-b (Complex from Homo sap)
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6wkr
Q-score: 0.362
Kasinath V, Beck C, Sauer P, Poepsel S, Kosmatka J, Faini M, Toso D, Aebersold R, Nogales E
Science (2021) 371 [ Pubmed: 33479123 DOI: doi:10.1126/science.abc3393 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Prc2-aebp2-jarid2 bound to h2ak119ub1 nucleosome (500 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Zinc finger protein aebp2 (33 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (85 kDa, Protein from Homo sapiens)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Prc2-aebp2-jarid2 (Complex from Homo sapiens)
- Dna (314-mer) (98 kDa, DNA from Homo sapiens)
- Protein jumonji (49 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- H2ak119ub1 nucleosome (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6inq
Q-score: 0.149
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 ]
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Rna (5'-r(p*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (3 kDa, RNA from synthetic construct)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Yeast)
- Rna polymerase ii subunit (18 kDa, Protein from Yeast)
- Histone h2a, histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Yeast)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Yeast)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Yeast)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Yeast)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Yeast)
- Histone h2b, histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Yeast)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Yeast)
- Zinc ion (65 Da, Ligand)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (+1 position) (Complex from Komagataella phaffii)
- Dna (198-mer) (38 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Yeast)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Yeast)
Cryo-EM structure of the human INO80 complex bound to nucleosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6hts
Q-score: 0.181
Ayala R, Willhoft O, Aramayo RJ, Wilkinson M, McCormack EA, Ocloo L, Wigley DB, Zhang X
Nature (2018) 556 pp. 391-395 [ DOI: doi:10.1038/s41586-018-0021-6 Pubmed: 29643506 ]
- Human ino80 (Complex from synthetic construct)
- Ino80 complex subunit b (38 kDa, Protein from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone subunits (Complex from Homo sapiens)
- Dna (142-mer) (62 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (142-mer) (61 kDa, DNA from synthetic construct)
- Nucleosome (Complex from Homo sapiens)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Complex of core human ino80 with nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna helicase ino80 (146 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
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)