Structure of DDM1-nucleosome complex in the apo state
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8wh5
Q-score: 0.394
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (51 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in the apo state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (sense strand) (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in ADP state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8wh8
Q-score: 0.403
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in ADP-BeFx state
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 8wh9
Q-score: 0.336
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Resolution: 4.05 Å
EM Method: Single-particle
Fitted PDBs: 8wha
Q-score: 0.306
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of nucleosome core particle of Arabidopsis thaliana
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 8whb
Q-score: 0.5
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Structure of the nucleosome core particle of arabidopsis thaliana (200 kDa, Complex from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Dna (sense strand) (45 kDa, DNA from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of inner kinetochore CCAN-Cenp-A complex
Resolution: 4.15 Å
EM Method: Single-particle
Fitted PDBs: 6qld
Q-score: 0.328
Yan K, Yang J, Zhang Z, McLaughlin SH, Chang L, Fasci D, Ehrenhofer-Murray AE, Heck AJR, Barford D
Nature (2019) 574 pp. 278-282 [ Pubmed: 31578520 DOI: doi:10.1038/s41586-019-1609-1 ]
- Histone h2b.1 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit mcm16 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Kinetochore (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae)
- Histones (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit nkp1 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit mcm21 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit ame1 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.2 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit chl4 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (125-mer) (38 kDa, DNA from Escherichia coli)
- Inner kinetochore subunit mif2 (2 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3-like centromeric protein cse4 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore ccan complex assembled onto a centromeric nucleosome (Complex)
- Inner kinetochore subunit okp1 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3-like centromeric protein cse4 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit ctf3 (47 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (125-mer) (38 kDa, DNA from Escherichia coli)
- Inner kinetochore subunit nkp2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit iml3 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from Escherichia coli)
- Inner kinetochore subunit ctf19 (31 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inner kinetochore subunit mcm22 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))