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 [ DOI: doi:10.1038/s41477-024-01640-z Pubmed: 38413824 ]
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 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 ]
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- 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 ]
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Cryo-EM structure of Arabidopsis DCL3 in complex with a 40-bp RNA
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7vg2
Q-score: 0.545
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S, Jacobsen SE, Du J
Science (2021) 374 pp. 1152-1157 [ Pubmed: 34648373 DOI: doi:10.1126/science.abl4546 ]
- Rna (Complex)
- Dcl3 in complex with a 40-bp rna (210 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Tas1a forward strand (5'-phosphorylation) (12 kDa, RNA from Arabidopsis thaliana)
- Dicer-like 3 (182 kDa, Protein from Arabidopsis thaliana)
- Tas1a reverse strand (13 kDa, RNA from Arabidopsis thaliana)
- Dcl3 (Complex from Arabidopsis thaliana)
- Calcium ion (40 Da, Ligand)
Cryo-EM structure of Arabidopsis DCL3 in complex with a 30-bp RNA
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 7vg3
Q-score: 0.462
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S, Jacobsen SE, Du J
Science (2021) 374 pp. 1152-1157 [ DOI: doi:10.1126/science.abl4546 Pubmed: 34648373 ]
- Tas1a rna reverse strand (10 kDa, RNA from Arabidopsis thaliana)
- Dcl3 in complex with a 30-bp rna (200 kDa, Complex)
- Dcl3 (Complex from Arabidopsis thaliana)
- Zinc ion (65 Da, Ligand)
- Dicer-like 3 (182 kDa, Protein from Arabidopsis thaliana)
- Rna (Complex)
- Tas1a rna forward strand (5'-phosphorylated) (9 kDa, RNA from Arabidopsis thaliana)
- Calcium ion (40 Da, Ligand)