Structure of nucleosome-DI complex (-30I, Apo state)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7xfc
Q-score: 0.569
Cell Discov (2023) 9 pp. 62-62 [ Pubmed: 37339965 DOI: doi:10.1038/s41421-023-00560-0 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (152-mer) (46 kDa, DNA from Xenopus laevis)
- Dna (152-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Complex (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
Structure of nucleosome-AAG complex (A-30I, post-catalytic state)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7xfh
Q-score: 0.515
Cell Discov (2023) 9 pp. 62-62 [ Pubmed: 37339965 DOI: doi:10.1038/s41421-023-00560-0 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-3-methyladenine glycosylase (Complex from Homo sapiens)
- Dna (152-mer) (46 kDa, DNA from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-3-methyladenine glycosylase (32 kDa, Protein from Homo sapiens)
- Dna (152-mer) (47 kDa, DNA from Xenopus laevis)
- Complex (Complex)
Structure of nucleosome-DI complex (-50I, Apo state)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7xfi
Q-score: 0.525
Cell Discov (2023) 9 pp. 62-62 [ Pubmed: 37339965 DOI: doi:10.1038/s41421-023-00560-0 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (152-mer) (47 kDa, DNA from Xenopus laevis)
- Complex (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (152-mer) (46 kDa, DNA from Xenopus laevis)
Structure of nucleosome-AAG complex (A-53I, free state)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7xfl
Q-score: 0.55
Cell Discov (2023) 9 pp. 62-62 [ Pubmed: 37339965 DOI: doi:10.1038/s41421-023-00560-0 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (152-mer) (46 kDa, DNA from Xenopus laevis)
- Dna (152-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Complex (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
Structure of nucleosome-DI complex (-55I, Apo state)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7xfn
Q-score: 0.55
Cell Discov (2023) 9 pp. 62-62 [ Pubmed: 37339965 DOI: doi:10.1038/s41421-023-00560-0 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (152-mer) (46 kDa, DNA from Xenopus laevis)
- Dna (152-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Complex (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vdt
Q-score: 0.549
Yuan JJ, Chen KJ, Zhang WB, Chen ZC
Nature (2022) 605 pp. 166-171 [ DOI: doi:10.1038/s41586-022-04658-5 Pubmed: 35477757 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (207-mer) (64 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- The motor-nucleosome module of human chromatin remodeling pbaf-nucleosome complex (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (207-mer) (63 kDa, DNA from synthetic construct)
- Isoform 2 of transcription activator brg1 (169 kDa, Protein from Homo sapiens)
RNA polymerase II-Spt4/5-nucleosome-Chd1 structure
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nkx
Q-score: 0.444
Farnung L, Ochmann M, Engeholm M, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 382-387 [ Pubmed: 33846633 DOI: doi:10.1038/s41594-021-00578-6 ]
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii-spt4/5-chd1-nucleosome (Complex)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (116 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (128-mer) (54 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (139-mer) (56 kDa, DNA from synthetic construct)
- Rna (21 kDa, RNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
nucleosome with TBP and TFIIA bound at SHL +2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7oha
Q-score: 0.516
PNAS (2021) 118 [ Pubmed: 34301908 DOI: doi:10.1073/pnas.2108859118 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (122-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (122-mer) (44 kDa, DNA from synthetic construct)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Nucleosome with tbp (230 kDa, Complex)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7ohc
Q-score: 0.587
PNAS (2021) 118 [ Pubmed: 34301908 DOI: doi:10.1073/pnas.2108859118 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nucleosome core particle (200 kDa, Complex)
The structure of ALC1 bound to the nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7enn
Q-score: 0.567
Nat Commun (2021) 12 pp. 4057-4057 [ Pubmed: 34210977 DOI: doi:10.1038/s41467-021-24320-4 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Histone (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Alc1 (Complex from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- The structure of alc1 bound to the nucleosome (Complex)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (101 kDa, Protein from Homo sapiens)