Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 8kcb
Q-score: 0.38
Zhang H, Gu Z, Zeng Y, Zhang Y
Structure (2024) 32 pp. 1222-1230.e4 [ DOI: doi:10.1016/j.str.2024.05.013 Pubmed: 38870940 ]
- Dna (170-mer) (52 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2b.10 (15 kDa, Protein from Arabidopsis thaliana)
- Complex of ddm1-nucleosome(h2a.w) complex with ddm1 bound to shl2 (Complex from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Dna (170-mer) (52 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8kcc
Q-score: 0.387
Zhang H, Gu Z, Zeng Y, Zhang Y
Structure (2024) 32 pp. 1222-1230.e4 [ DOI: doi:10.1016/j.str.2024.05.013 Pubmed: 38870940 ]
- Dna (170-mer) (52 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b.10 (15 kDa, Protein from Arabidopsis thaliana)
- Complex of ddm1-nucleosome(h2a.w) complex with ddm1 bound to shl2 (Complex from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (170-mer) (52 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Probable histone h2a.7 (15 kDa, Protein from Arabidopsis thaliana)
Structure of transcribing RNA polymerase II-nucleosome complex
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 6i84
Q-score: 0.241
Nat Commun (2018) 9 pp. 5432-5432 [ DOI: doi:10.1038/s41467-018-07870-y Pubmed: 30575770 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (38 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 (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (158-mer) (49 kDa, DNA from synthetic construct)
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (3 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (170-mer) (52 kDa, DNA from synthetic construct)
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex)
- Complex of s. cerevisiae rna polymerase ii and x. leaves ncp (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)