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 polymerase v (Complex from Brassica oleracea)
- Rpold domain-containing protein (35 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase v largest subunit (222 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 ii, iv and v subunit 12 (5 kDa, Protein from Brassica oleracea)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Brassica oleracea)
- Dna-dependent rna polymerase iv and v subunit 2 (132 kDa, Protein from Brassica oleracea)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Brassica oleracea)
- 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 rpabc3 (16 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Brassica oleracea)
- Zinc ion (65 Da, Ligand)
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 ]
- Dna (34-mer) (10 kDa, DNA from Brassica oleracea)
- 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 i, ii, and iii subunit rpabc5 (7 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (26 kDa, Protein 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 polymerases ii, iv and v subunit 12 (5 kDa, Protein from Brassica oleracea)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Brassica oleracea)
- Magnesium ion (24 Da, Ligand)
- 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-rna (Complex)
- 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)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Brassica oleracea)
- Dna-directed rna polymerase iv and v subunit 2 (132 kDa, Protein from Brassica oleracea)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of CasLambda (Cas12l) bound to crRNA and DNA
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8dc2
Q-score: 0.491
Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA
Cell (2022) 185 pp. 4574-4586.e16 [ DOI: doi:10.1016/j.cell.2022.10.020 Pubmed: 36423580 ]
- Dna nts (14 kDa, DNA from uncultured virus)
- Caslambda (87 kDa, Protein from uncultured virus)
- Caslambda-crrna-dsdna ternary structure (Complex from uncultured virus)
- Rna (51-mer) (16 kDa, RNA from uncultured virus)
- Dna ts (14 kDa, DNA from uncultured virus)
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)
- Tas1a forward strand (5'-phosphorylation) (12 kDa, RNA from Arabidopsis thaliana)
- Dcl3 (Complex from Arabidopsis thaliana)
- Calcium ion (40 Da, Ligand)
- Tas1a reverse strand (13 kDa, RNA from Arabidopsis thaliana)
- Dicer-like 3 (182 kDa, Protein from Arabidopsis thaliana)
- Dcl3 in complex with a 40-bp rna (210 kDa, Complex)
- Zinc ion (65 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 [ Pubmed: 34648373 DOI: doi:10.1126/science.abl4546 ]
- Rna (Complex)
- Dcl3 in complex with a 30-bp rna (200 kDa, Complex)
- Dcl3 (Complex from Arabidopsis thaliana)
- Tas1a rna forward strand (5'-phosphorylated) (9 kDa, RNA from Arabidopsis thaliana)
- Calcium ion (40 Da, Ligand)
- Tas1a rna reverse strand (10 kDa, RNA from Arabidopsis thaliana)
- Dicer-like 3 (182 kDa, Protein from Arabidopsis thaliana)
- Zinc ion (65 Da, Ligand)
CryoEM structure of Arabidopsis DR complex (DMS3-RDM1)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6ois
Q-score: 0.444
Wongpalee SP, Liu S, Gallego-Bartolome J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE
Nat Commun (2019) 10 pp. 3916-3916 [ Pubmed: 31477705 DOI: doi:10.1038/s41467-019-11759-9 ]
- Dr complex of dms3 with rdm1 (Complex from Arabidopsis thaliana)
- Protein rdm1 (20 kDa, Protein from Arabidopsis thaliana)
- Protein defective in meristem silencing 3 (49 kDa, Protein from Arabidopsis thaliana)
CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6oit
Q-score: 0.466
Wongpalee SP, Liu S, Gallego-Bartolome J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE
Nat Commun (2019) 10 pp. 3916-3916 [ Pubmed: 31477705 DOI: doi:10.1038/s41467-019-11759-9 ]
- Protein rdm1 (20 kDa, Protein from Arabidopsis thaliana)
- Protein defective in meristem silencing 3 (49 kDa, Protein from Arabidopsis thaliana)
- Protein chromatin remodeling 35 (7 kDa, Protein from Arabidopsis thaliana)
- Ddr' complex of drd1 peptide with dms3 and rdm1 (Complex from Arabidopsis thaliana)
A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase
Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X, Bernatavichute Y, Cheng Y, Jacobsen SE, Narlikar GJ
Mol Cell (2019) 73 pp. 73-83.e6 [ DOI: doi:10.1016/j.molcel.2018.10.006 Pubmed: 30415948 ]