A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8hil
Q-score: 0.461
Xie G, Du X, Hu H, Li S, Cao X, Jacobsen SE, Du J
Science (2023) 379 pp. 1209-1213 [ DOI: doi:10.1126/science.adf8231 Pubmed: 36893216 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (16 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (26 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Brassica oleracea)
- Zinc ion (65 Da, Ligand)
- Rpold domain-containing protein (35 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Brassica oleracea)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase v (Complex from Brassica oleracea)
- Dna-directed rna polymerase v largest subunit (222 kDa, Protein from Brassica oleracea)
- Dna-dependent rna polymerase iv and v subunit 2 (132 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Brassica oleracea)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Brassica oleracea)
A cryo-EM structure of B. oleracea RNA polymerase V elongation complex at 2.73 Angstrom
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8him
Q-score: 0.543
Xie G, Du X, Hu H, Li S, Cao X, Jacobsen SE, Du J
Science (2023) 379 pp. 1209-1213 [ DOI: doi:10.1126/science.adf8231 Pubmed: 36893216 ]
- Rna (5'-r(*up*ap*up*ap*up*gp*cp*ap*up*ap*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3') (6 kDa, RNA from Brassica oleracea)
- Dna-directed rna polymerase (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (16 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase iv and v subunit 2 (132 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (26 kDa, Protein from Brassica oleracea)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Brassica oleracea)
- Dna (34-mer) (10 kDa, DNA from Brassica oleracea)
- Dna-rna (Complex)
- Dna-directed rna polymerase v elongation complex (Complex from Brassica oleracea)
- Dna-directed rna polymerase v largest subunit (222 kDa, Protein from Brassica oleracea)
- Rpold domain-containing protein (35 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Brassica oleracea)
- Magnesium ion (24 Da, Ligand)
- Dna (34-mer) (10 kDa, DNA from Brassica oleracea)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Brassica oleracea)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Brassica oleracea)
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 [ DOI: doi:10.1038/s41477-022-01322-8 Pubmed: 36624257 ]
- Ros1-tg mismatch dsdna complex (Complex)
- Sex-determining region y protein,dna glycosylase/ap lyase ros1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Ros1 (Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Tg mismatch dsdna (Complex 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 [ DOI: doi:10.1038/s41477-022-01322-8 Pubmed: 36624257 ]
- 5mc dsdna (Complex from Arabidopsis thaliana)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Sex-determining region y protein,repressor of silencing 1,dna glycosylase/ap lyase ros1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Ros1-5mc dsdna complex (Complex)
- Ros1 (Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
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 [ DOI: doi:10.1038/s41477-022-01322-8 Pubmed: 36624257 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dsdna (Complex from Arabidopsis thaliana)
- Ros1 (Complex from Homo sapiens)
- Sex-determining region y protein,dna glycosylase/ap lyase ros1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
- Covalent-linked reaction intermediate of arabidopsis ros1 with dsdna (Complex)
- Dna (40-mer) (12 kDa, DNA from Arabidopsis thaliana)
CryoEM structure of apo form ZmRDR2 at 3.4 Angstroms resolution
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7w84
Q-score: 0.438
Du X, Yang Z, Ariza AJF, Wang Q, Xie G, Li S, Du J
Plant Cell (2022) 34 pp. 2140-2149 [ DOI: doi:10.1093/plcell/koac067 Pubmed: 35188193 ]
- Rna-dependent rna polymerase 2 in apo form (Cellular component from Zea mays)
- Rna-dependent rna polymerase (126 kDa, Protein from Zea mays)
CryoEM structure of open form ZmRDR2 at 3.5 Angstroms resolution
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7w88
Q-score: 0.422
Du X, Yang Z, Ariza AJF, Wang Q, Xie G, Li S, Du J
Plant Cell (2022) 34 pp. 2140-2149 [ Pubmed: 35188193 DOI: doi:10.1093/plcell/koac067 ]
- Rna-dependent rna polymerase 2 in open form (Cellular component from Zea mays)
- Rna-dependent rna polymerase (126 kDa, Protein from Zea mays)