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GK monomer complexes with catalytic intermediate
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8j0e
Q-score: 0.473
To Be Published
- Arabidopsis thaliana p5csb incubated with all substrates. (Complex from Arabidopsis thaliana)
- Delta-1-pyrroline-5-carboxylate synthase b (78 kDa, Protein from Arabidopsis thaliana)
- (2~{r})-5-[[[[(2~{r},3~{s},4~{s},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-azanyl-5-oxidanylidene-pentanoic acid (636 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
GK tetramer with adjacent hooks at reaction state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8j0f
Q-score: 0.456
To Be Published
- 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)
- Delta-1-pyrroline-5-carboxylate synthase b (78 kDa, Protein from Arabidopsis thaliana)
GK monomer complexes with glutamate and ATP
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8j0g
Q-score: 0.411
To Be Published
- Gamma-l-glutamic acid (147 Da, Ligand)
- Arabidopsis thaliana p5csb incubated with all substrates. (Complex from Arabidopsis thaliana)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Delta-1-pyrroline-5-carboxylate synthase b (78 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8j27
Q-score: 0.4
To Be Published
GK monomer complexes with G5P and ADP
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8j28
Q-score: 0.411
To Be Published
- Arabidopsis thaliana p5csb incubated with all substrates. (Complex from Arabidopsis thaliana)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Delta-1-pyrroline-5-carboxylate synthase b (78 kDa, Protein from Arabidopsis thaliana)
- Gamma-glutamyl phosphate (227 Da, Ligand)
Structure of DDM1-nucleosome complex in the apo state
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 apo state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (51 kDa, DNA from synthetic construct)
- 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)
- 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 ]
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 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)
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b.6 (16 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 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 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)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex 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 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 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)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 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 h2b.6 (16 kDa, Protein 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 ]
- Dna (sense strand) (45 kDa, DNA from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein 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)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Structure of the nucleosome core particle of arabidopsis thaliana (200 kDa, Complex from Arabidopsis thaliana)