GK tetramer of AtP5CS1 filament with adjacent hooks, reaction state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8y2h
Q-score: 0.471
Guo CJ, Zhang T, Leng Q, Zhou X, Zhong J, Liu JL
Nat Plants (2024) [ DOI: doi:10.1038/s41477-024-01697-w Pubmed: 38740943 ]
- Arabidopsis thaliana p5csa incubated with all substrates. (78 MDa, Complex from Arabidopsis thaliana)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Delta-1-pyrroline-5-carboxylate synthase a (78 kDa, Protein from Arabidopsis thaliana)
GK tetramer with adjacent hooks at reaction state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8j0f
Q-score: 0.456
Guo CJ, Zhang T, Leng Q, Zhou X, Zhong J, Liu JL
Nat Plants (2024) [ DOI: doi:10.1038/s41477-024-01697-w Pubmed: 38740943 ]
- Delta-1-pyrroline-5-carboxylate synthase b (78 kDa, Protein from Arabidopsis thaliana)
- Gamma-glutamyl phosphate (227 Da, Ligand)
- Arabidopsis thaliana p5csb incubated with all substrates. (78 MDa, Complex from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
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 ]
- 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) (51 kDa, DNA from synthetic construct)
- Dna (antisense strand) (51 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in the apo state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 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 [ 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 [ DOI: doi:10.1038/s41477-024-01640-z Pubmed: 38413824 ]
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex from Arabidopsis thaliana)
- 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)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 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 ]
- 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)
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 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 ]
- Structure of the nucleosome core particle of arabidopsis thaliana (200 kDa, Complex from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein 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 ]
- Cholesterol hemisuccinate (486 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Phosphatidylinositol (887 Da, Ligand)
- Water (18 Da, Ligand)
- Cation transporter hkt2;1 (60 kDa, Protein from Oryza sativa subsp. japonica)
- Cholesterol (386 Da, Ligand)
- Oshkt2;1 dimer (Complex 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 ]
- Cholesterol hemisuccinate (486 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Phosphatidylinositol (887 Da, Ligand)
- Water (18 Da, Ligand)
- Oshkt2;2/1 dimer (Complex from Oryza sativa subsp. indica)
- Cholesterol (386 Da, Ligand)
- Cation transporter hkt2;2 (60 kDa, Protein from Oryza sativa subsp. indica)
Apo state of Arabidopsis AZG1 at pH 7.4
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8irl
Q-score: 0.604
Xu L, Jia W, Tao X, Ye F, Zhang Y, Ding ZJ, Zheng SJ, Qiao S, Su N, Zhang Y, Wu S, Guo J
Nat Plants (2024) 10 pp. 180-191 [ DOI: doi:10.1038/s41477-023-01590-y Pubmed: 38172575 ]
- Azg1 dimer (131 kDa, Complex from Arabidopsis thaliana)
- Adenine/guanine permease azg1 (65 kDa, Protein from Arabidopsis thaliana)