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) 52 pp. 6718-6727 [ Pubmed: 38742627 DOI: doi:10.1093/nar/gkae395 ]
- Cholesterol (386 Da, Ligand)
- Rna (Complex from Arabidopsis thaliana)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Rna (50-mer) (15 kDa, RNA from Arabidopsis thaliana)
- Systemic rna interference defective protein 1 (90 kDa, Protein from Caenorhabditis elegans)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Complex of sid1 and dsrna (Complex)
- Sid1 (Complex from Caenorhabditis elegans)
- Rna (50-mer) (16 kDa, RNA from Arabidopsis thaliana)
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 [ DOI: doi:10.1038/s41594-023-00989-7 Pubmed: 37127820 ]
- 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 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)
- Pri-mirna 166f (47 kDa, RNA from Arabidopsis thaliana)
- Endoribonuclease dicer homolog 1 (213 kDa, Protein 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)
Structure of the plant mitochondrial ribosome
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 6xyw
Q-score: 0.359
Waltz F, Soufari H, Bochler A, Giege P, Hashem Y
Nat Plants (2020) 6 pp. 377-383 [ Pubmed: 32251374 DOI: doi:10.1038/s41477-020-0631-5 ]
- At4g31460/f3l17_30 (24 kDa, Protein from thale cress)
- 50s ribosomal protein l21, mitochondrial (30 kDa, Protein from thale cress)
- At5g09770 (18 kDa, Protein from thale cress)
- Ribosomal protein l25/gln-trna synthetase, anti-codon-binding domain-containing protein (27 kDa, Protein from thale cress)
- At1g73940/f2p9_19 (17 kDa, Protein from thale cress)
- Pentatricopeptide repeat-containing protein pnm1, mitochondrial (59 kDa, Protein from thale cress)
- Ribosomal protein s21 family protein (11 kDa, Protein from thale cress)
- 28s ribosomal s34 protein (15 kDa, Protein from thale cress)
- Gb|aac32909.1 (48 kDa, Protein from thale cress)
- 39s ribosomal protein (14 kDa, Protein from thale cress)
- At5g27820 (12 kDa, Protein from thale cress)
- 30s ribosomal protein s16-2, chloroplastic/mitochondrial (15 kDa, Protein from thale cress)
- At4g05400 (27 kDa, Protein from thale cress)
- At4g35490 (16 kDa, Protein from thale cress)
- At3g18240 protein (48 kDa, Protein from thale cress)
- Ribosomal protein s4, mitochondrial (43 kDa, Protein from thale cress)
- 40s ribosomal protein s19, mitochondrial (23 kDa, Protein from thale cress)
- Small ribosomal subunit protein s13, mitochondrial (17 kDa, Protein from thale cress)
- At1g52370 protein (30 kDa, Protein from thale cress)
- 30s ribosomal protein s9, mitochondrial (48 kDa, Protein from thale cress)
- Unk-5 (6 kDa, Protein from thale cress)
- Rppr* (24 kDa, Protein from thale cress)
- At1g15810/f7h2_23 (47 kDa, Protein from thale cress)
- Probable ribosomal protein s11, mitochondrial (33 kDa, Protein from thale cress)
- Unk-3 (4 kDa, Protein from thale cress)
- 30s ribosomal protein s31, mitochondrial (10 kDa, Protein from thale cress)
- At1g64880 (60 kDa, Protein from thale cress)
- At5g26800 (12 kDa, Protein from thale cress)
- Ribosomal protein s12, mitochondrial (14 kDa, Protein from thale cress)
- 60s ribosomal protein l16, mitochondrial (20 kDa, Protein from thale cress)
- Pentatricopeptide repeat-containing protein at1g60770 (55 kDa, Protein from thale cress)
- 3-hydroxyisobutyryl-coa hydrolase-like protein 2, mitochondrial (45 kDa, Protein from thale cress)
- Ribosomal protein l18e/l15 superfamily protein (31 kDa, Protein from thale cress)
- Rppr* (22 kDa, Protein from thale cress)
- Ribosomal protein l31 (8 kDa, Protein from thale cress)
- At5g55140 (12 kDa, Protein from thale cress)
- Rna (118-mer) (37 kDa, RNA from thale cress)
- 50s ribosomal protein l24 (17 kDa, Protein from thale cress)
- Mitochondrial ribosomal protein l51/s25/ci-b8 family protein (16 kDa, Protein from thale cress)
- Expressed protein (22 kDa, Protein from thale cress)
- At4g39880 (19 kDa, Protein from thale cress)
- F10k1.8 protein (29 kDa, Protein from thale cress)
- 60s ribosomal protein l2, mitochondrial (37 kDa, Protein from thale cress)
- Ribosomal protein s7, mitochondrial (17 kDa, Protein from thale cress)
- The large mitoribosomal subunit of the plant mitoribosome (Complex from Arabidopsis thaliana)
- 50s ribosomal protein l4 (33 kDa, Protein from thale cress)
- Unk-1 (4 kDa, Protein from thale cress)
- Rppr* (18 kDa, Protein from thale cress)
- At1g07830/f24b9_7 (16 kDa, Protein from thale cress)
- Translation elongation factor ef1b/ribosomal protein s6 family protein (15 kDa, Protein from thale cress)
- At5g40080 (10 kDa, Protein from thale cress)
- Cx9c domain-containing protein (10 kDa, Protein from thale cress)
- Ms31/ms46 (8 kDa, Protein from thale cress)
- 50s ribosomal protein l27 (16 kDa, Protein from thale cress)
- Ribosomal protein s2, mitochondrial (24 kDa, Protein from thale cress)
- At3g06320 (6 kDa, Protein from thale cress)
- 40s ribosomal protein s10, mitochondrial (27 kDa, Protein from thale cress)
- 50s ribosomal protein l3-2, mitochondrial (35 kDa, Protein from thale cress)
- 50s ribosomal protein hlp, mitochondrial (18 kDa, Protein from thale cress)
- Ribosomal protein l9/rnase h1 (25 kDa, Protein from thale cress)
- At1g14620/t5e21_15 (27 kDa, Protein from thale cress)
- At1g24240/f3i6_17 (25 kDa, Protein from thale cress)
- Ribosomal protein (11 kDa, Protein from thale cress)
- Nucleic acid-binding, ob-fold-like protein (12 kDa, Protein from thale cress)
- At4g22000 (15 kDa, Protein from thale cress)
- 60s ribosomal protein l5, mitochondrial (21 kDa, Protein from thale cress)
- At1g26740/t24p13_11 (14 kDa, Protein from thale cress)
- Rna (2842-mer) (918 kDa, RNA from thale cress)
- Ms38 (15 kDa, Protein from thale cress)
- 50s ribosomal protein l20 (14 kDa, Protein from thale cress)
- Pentatricopeptide repeat-containing protein at3g02650, mitochondrial (63 kDa, Protein from thale cress)
- At3g51010 (21 kDa, Protein from thale cress)
- At5g49210/k21p3_8 (23 kDa, Protein from thale cress)
- At2g34520 (18 kDa, Protein from thale cress)
- 40s ribosomal protein s15a-5 (14 kDa, Protein from thale cress)
- Putative ribosomal protein l6 (11 kDa, Protein from thale cress)
- Unk-4 (2 kDa, Protein from thale cress)
- At1g01640 (23 kDa, Protein from thale cress)
- 50s ribosomal protein l10 (19 kDa, Protein from thale cress)
- Ribosomal protein s3, mitochondrial (64 kDa, Protein from thale cress)
- Uncharacterized protein (22 kDa, Protein from thale cress)
- Rna (1743-mer) (564 kDa, RNA from thale cress)
- Unk-6 (2 kDa, Protein from thale cress)
- Uncharacterized protein at1g27435/f17l21.30 (8 kDa, Protein from thale cress)
- Mitochondrial 28s ribosomal protein s29-like protein (53 kDa, Protein from thale cress)
- 37s ribosomal protein s27 (11 kDa, Protein from thale cress)
- Rppr* (47 kDa, Protein from thale cress)
- Adenylyl cyclase (43 kDa, Protein from thale cress)
- Ribosomal protein l35 (20 kDa, Protein from thale cress)
- Unk-2 (5 kDa, Protein from thale cress)