Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 8yny
Q-score: 0.218
Nagamura R, Kujirai T, Kato J, Shuto Y, Kusakizako T, Hirano H, Endo M, Toki S, Saika H, Kurumizaka H, Nureki O
Nat Commun (2024) 15 pp. 10744-10744 [ DOI: doi:10.1038/s41467-024-54768-z Pubmed: 39737984 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Spcas9-sgrna-nucleosome ternary complex (Complex from Homo sapiens)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Dna (175-mer) (53 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (176-mer) (54 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (17-mer) (5 kDa, DNA from Homo sapiens)
- Rna (97-mer) (31 kDa, RNA from Streptococcus pyogenes)
Rpd3S bound to an H3K36Cme3 modified nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8tof
Q-score: 0.464
Nat Commun (2023) 14 pp. 8128-8128 [ Pubmed: 38065958 DOI: doi:10.1038/s41467-023-43968-8 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone n-terminal tail (657 Da, Protein from Xenopus laevis)
- Dna (176-mer) (63 kDa, DNA from synthetic construct)
- Rco1 (515 Da, Protein from Saccharomyces cerevisiae)
- Rpd3s bound to h3k36cme3 nucleosome (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (66 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Nucleosome 1 of the 4x177 nucleosome array containing H1
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7pew
Q-score: 0.29
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Nucleosome 1 from 4x177 nucleosome array (Complex)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Dna (176-mer) (53 kDa, DNA from synthetic construct)
- Dna (176-mer) (54 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 6g0l
Q-score: 0.095
Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T
eLife (2018) 7 [ DOI: doi:10.7554/eLife.35720 Pubmed: 30079888 ]
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (Complex from Xenopus laevis)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (Complex from Saccharomyces cerevisiae S288C)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (176-mer) (54 kDa, DNA from synthetic construct)
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (600 kDa, Complex)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (Complex from synthetic construct)