C. elegans SID1 in complex with dsRNA
Resolution: 2.21 Å
EM Method: Single-particle
Fitted PDBs: 8xc1
Q-score: 0.566
Wang R, Cong Y, Qian D, Yan C, Gong D
Nucleic Acids Res (2024) [ DOI: doi:10.1093/nar/gkae395 Pubmed: 38742627 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Complex of sid1 and dsrna (Complex)
- Sid1 (Complex from Caenorhabditis elegans)
- Zinc ion (65 Da, Ligand)
- Rna (Complex from Arabidopsis thaliana)
- Rna (50-mer) (15 kDa, RNA from Arabidopsis thaliana)
- Systemic rna interference defective protein 1 (90 kDa, Protein from Caenorhabditis elegans)
- Cholesterol (386 Da, Ligand)
- Rna (50-mer) (16 kDa, RNA from Arabidopsis thaliana)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8hyj
Q-score: 0.205
Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y
Nat Commun (2023) 14 pp. 3118-3118 [ Pubmed: 37253723 DOI: doi:10.1038/s41467-023-38619-x ]
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 3b (35 kDa, Protein from Arabidopsis thaliana)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases ii and v subunit 8a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Ktf1-bound polymerase v transcription elongation complex (608 MDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases iv and v subunit 4 (22 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase v subunit 1 (218 kDa, Protein from Arabidopsis thaliana)
- Protein rna-directed dna methylation 3 (158 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerase v subunit 7 (20 kDa, Protein from Arabidopsis thaliana)
- Rna (30-mer) (9 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase v subunit 5a (25 kDa, Protein from Arabidopsis thaliana)
Cryo-EM structure of Arabidopsis Ago10-guide RNA complex
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 7sva
Q-score: 0.462
Xiao Y, Maeda S, Otomo T, MacRae IJ
Nat Struct Mol Biol (2023) 30 pp. 778-784 [ Pubmed: 37127820 DOI: doi:10.1038/s41594-023-00989-7 ]
- Magnesium ion (24 Da, Ligand)
- Protein argonaute 10 (110 kDa, Protein from Arabidopsis thaliana)
- Atago10-guide rna complex (Complex from Arabidopsis thaliana)
- Rna (5'-r(p*up*gp*gp*ap*gp*up*gp*up*gp*ap*cp*ap*ap*up*gp*gp*up*gp*up*up*u)-3') (6 kDa, RNA from synthetic construct)
Cryo-EM structure of Arabidopsis Ago10-guide-target RNA complex in a bent duplex conformation
Resolution: 3.79 Å
EM Method: Single-particle
Fitted PDBs: 7swq
Q-score: 0.41
Xiao Y, Maeda S, Otomo T, MacRae IJ
Nat Struct Mol Biol (2023) 30 pp. 778-784 [ Pubmed: 37127820 DOI: doi:10.1038/s41594-023-00989-7 ]
- Protein argonaute 10 (110 kDa, Protein from Arabidopsis thaliana)
- Atago10-guide-target rna complex (Complex from Arabidopsis thaliana)
- Rna (5'-r(p*up*gp*gp*ap*gp*up*gp*up*gp*ap*cp*ap*ap*up*gp*gp*up*gp*up*up*u)-3') (6 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*cp*cp*ap*up*up*gp*up*cp*ap*cp*ap*cp*up*cp*cp*ap*ap*a)-3') (5 kDa, RNA from synthetic construct)
Cryo-EM structure of Arabidopsis Ago10-guide-target RNA complex in a central duplex conformation
Resolution: 3.79 Å
EM Method: Single-particle
Fitted PDBs: 7swf
Q-score: 0.403
Nucleic Acids Res (2022) 50 pp. 10041-10052 [ Pubmed: 35801914 DOI: doi:10.1093/nar/gkac571 ]
- Protein argonaute 10 (110 kDa, Protein from Arabidopsis thaliana)
- Atago10-guide-target rna complex (Complex from Arabidopsis thaliana)
- Rna (5'-r(p*cp*cp*ap*up*up*gp*up*cp*ap*cp*ap*cp*up*cp*cp*ap*a)-3') (5 kDa, RNA from unidentified)
- Rna (5'-r(p*up*gp*gp*ap*gp*up*gp*up*gp*ap*cp*ap*ap*up*gp*gp*u)-3') (6 kDa, RNA from unidentified)
- Magnesium ion (24 Da, Ligand)
The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 7eu0
Q-score: 0.487
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science (2021) 374 pp. 1579-1586 [ Pubmed: 34941388 DOI: doi:10.1126/science.abj9184 ]
- Rna-dependent rna polymerase 2 (129 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from Arabidopsis thaliana)
- A. thaliana pol iv-rdr2 backtracked complex (550 kDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Arabidopsis thaliana)
- Dna (33-mer) (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Arabidopsis thaliana)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Arabidopsis thaliana)
- Dna (5'-d(*cp*tp*gp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*gp*ap*gp*tp*g)-3') (6 kDa, DNA from synthetic construct)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (39-mer) (12 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase iv subunit 1 (169 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Arabidopsis thaliana)
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)
- Dcl3 in complex with a 40-bp rna (210 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Tas1a forward strand (5'-phosphorylation) (12 kDa, RNA from Arabidopsis thaliana)
- Dicer-like 3 (182 kDa, Protein from Arabidopsis thaliana)
- Tas1a reverse strand (13 kDa, RNA from Arabidopsis thaliana)
- Dcl3 (Complex from Arabidopsis thaliana)
- Calcium ion (40 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)
- Tas1a rna forward strand (5'-phosphorylated) (9 kDa, RNA from Arabidopsis thaliana)
- Dcl3 in complex with a 30-bp rna (200 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Dicer-like 3 (182 kDa, Protein from Arabidopsis thaliana)
- Tas1a rna reverse strand (10 kDa, RNA from Arabidopsis thaliana)
- Dcl3 (Complex from Arabidopsis thaliana)
- Calcium ion (40 Da, Ligand)
Cryo-EM structure of Arabidopsis DCL1 in complex with pri-miRNA 166f
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7eld
Q-score: 0.157
Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y
Nat Plants (2021) 7 pp. 1389-1396 [ Pubmed: 34593993 DOI: doi:10.1038/s41477-021-01000-1 ]
- Binary complex of dcl1 in complex with pri-mirna 166f (Complex from Arabidopsis thaliana)
- Endoribonuclease dicer homolog 1 (213 kDa, Protein from Arabidopsis thaliana)
- Pri-mirna 166f (47 kDa, RNA from Arabidopsis thaliana)
Cryo-EM structure of Arabidopsis DCL1 in complex with pre-miRNA 166f
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 7ele
Q-score: 0.186
Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y
Nat Plants (2021) 7 pp. 1389-1396 [ Pubmed: 34593993 DOI: doi:10.1038/s41477-021-01000-1 ]
- Binary complex of dcl1 in complex with pre-mirna 166f (Complex from Arabidopsis thaliana)
- Pre-mirna 166f (28 kDa, RNA from Arabidopsis thaliana)
- Endoribonuclease dicer homolog 1 (213 kDa, Protein from Arabidopsis thaliana)