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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 [ DOI: doi:10.1038/s41477-024-01640-z Pubmed: 38413824 ]
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in the apo state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (51 kDa, DNA from synthetic construct)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (51 kDa, DNA from synthetic construct)
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 ]
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 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 [ DOI: doi:10.1038/s41477-024-01640-z Pubmed: 38413824 ]
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 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 [ DOI: doi:10.1038/s41477-024-01640-z Pubmed: 38413824 ]
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 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 [ DOI: doi:10.1038/s41477-024-01640-z Pubmed: 38413824 ]
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Structure of the nucleosome core particle of arabidopsis thaliana (200 kDa, Complex from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from Arabidopsis thaliana)
Cryo-EM structure of Oryza sativa HKT2;1 at 2.5 angstrom
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8k66
Q-score: 0.66
Wang X, Shen X, Qu Y, Zhang H, Wang C, Yang F, Shen H
Nat Plants (2024) 10 pp. 633-644 [ Pubmed: 38570642 DOI: doi:10.1038/s41477-024-01665-4 ]
- Phosphatidylinositol (887 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Oshkt2;1 dimer (Complex from Oryza sativa subsp. japonica)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Cation transporter hkt2;1 (60 kDa, Protein from Oryza sativa subsp. japonica)
Cryo-EM structure of Oryza sativa HKT2;2/1 at 2.3 angstrom
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8k69
Q-score: 0.692
Wang X, Shen X, Qu Y, Zhang H, Wang C, Yang F, Shen H
Nat Plants (2024) 10 pp. 633-644 [ Pubmed: 38570642 DOI: doi:10.1038/s41477-024-01665-4 ]
- Phosphatidylinositol (887 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Cation transporter hkt2;2 (60 kDa, Protein from Oryza sativa subsp. indica)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Oshkt2;2/1 dimer (Complex from Oryza sativa subsp. indica)
CryoEM structure of Arabidopsis ROS1 in complex with TG mismatch dsDNA at 3.3 Angstroms resolution
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7yho
Q-score: 0.432
Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J
Nat Plants (2023) 9 pp. 271-279 [ Pubmed: 36624257 DOI: doi:10.1038/s41477-022-01322-8 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Ros1-tg mismatch dsdna complex (Complex)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Tg mismatch dsdna (Complex from Arabidopsis thaliana)
- Sex-determining region y protein,dna glycosylase/ap lyase ros1 (86 kDa, Protein from Arabidopsis thaliana)
- Ros1 (Complex from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at 3.1 Angstroms resolution
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7yhp
Q-score: 0.526
Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J
Nat Plants (2023) 9 pp. 271-279 [ Pubmed: 36624257 DOI: doi:10.1038/s41477-022-01322-8 ]
- Ros1-5mc dsdna complex (Complex)
- 5mc dsdna (Complex from Arabidopsis thaliana)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Ros1 (Complex from Homo sapiens)
- Sex-determining region y protein,repressor of silencing 1,dna glycosylase/ap lyase ros1 (86 kDa, Protein from Arabidopsis thaliana)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7yhq
Q-score: 0.377
Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J
Nat Plants (2023) 9 pp. 271-279 [ Pubmed: 36624257 DOI: doi:10.1038/s41477-022-01322-8 ]
- Covalent-linked reaction intermediate of arabidopsis ros1 with dsdna (Complex)
- Sex-determining region y protein,dna glycosylase/ap lyase ros1 (86 kDa, Protein from Arabidopsis thaliana)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Dsdna (Complex from Arabidopsis thaliana)
- Ros1 (Complex from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)