DmDcr-2/R2D2/LoqsPD with 50bp-dsRNA in Dimer state
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8hf0
Q-score: 0.372
Deng T, Su S, Yuan X, He J, Huang Y, Ma J, Wang J
Nat Commun (2023) 14 pp. 5228-5228 [ Pubmed: 37633971 DOI: doi:10.1038/s41467-023-40919-1 ]
- Dmdcr-2/r2d2/loqspd with 50bp-dsrna in dimer state (300 kDa, Complex from Drosophila melanogaster)
- Ld06392p (35 kDa, Protein from Drosophila melanogaster)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
- Rna (52-mer) (16 kDa, RNA from Drosophila melanogaster)
DmDcr-2/R2D2/LoqsPD with 19bp-dsRNA in Trimer state
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8hf1
Q-score: 0.307
Deng T, Su S, Yuan X, He J, Huang Y, Ma J, Wang J
Nat Commun (2023) 14 pp. 5228-5228 [ Pubmed: 37633971 DOI: doi:10.1038/s41467-023-40919-1 ]
- Dicer-2, isoform a (197 kDa, Protein from Drosophila melanogaster)
- Loquacious, isoform d (2 kDa, Protein from Drosophila melanogaster)
- Dmdcr-2/r2d2/loqspd with 19bp-dsrna in trimer state (300 kDa, Complex from Drosophila melanogaster)
- Rna (5'-r(p*cp*cp*ap*ap*gp*up*cp*up*cp*up*u)-3') (3 kDa, RNA from Drosophila melanogaster)
- Ld06392p (14 kDa, Protein from Drosophila melanogaster)
- Rna (5'-r(p*gp*ap*gp*ap*cp*up*up*gp*g)-3') (2 kDa, RNA from Drosophila melanogaster)
dmDicer2-LoqsPD-dsRNA Dimer status
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 7w0a
Q-score: 0.51
Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J
Nature (2022) 607 pp. 399-406 [ Pubmed: 35768513 DOI: doi:10.1038/s41586-022-04911-x ]
- Dicer2-loqspd-dsrna complex at its initial binding state (Complex from Drosophila melanogaster)
- Rna (30-mer) (10 kDa, RNA from Drosophila melanogaster)
- Rna (32-mer) (10 kDa, RNA from Spodoptera frugiperda)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
Dicer2-LoqsPD complex at apo status
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7w0b
Q-score: 0.339
Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J
Nature (2022) 607 pp. 399-406 [ Pubmed: 35768513 DOI: doi:10.1038/s41586-022-04911-x ]
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
- Dicer2-loqspd complex at its apo status (Complex from Drosophila melanogaster)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
Dicer2-Loqs-PD-dsRNA complex at early-translocation state
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7w0c
Q-score: 0.339
Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J
Nature (2022) 607 pp. 399-406 [ Pubmed: 35768513 DOI: doi:10.1038/s41586-022-04911-x ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dicer2-loqspd-dsrna complex at its early-translocation state (Complex from Drosophila melanogaster)
- Magnesium ion (24 Da, Ligand)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
- Rna (35-mer) (16 kDa, RNA from Drosophila melanogaster)
Dicer2-LoqsPD-dsRNA complex at mid-translocation state
Resolution: 4.18 Å
EM Method: Single-particle
Fitted PDBs: 7w0d
Q-score: 0.318
Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J
Nature (2022) 607 pp. 399-406 [ Pubmed: 35768513 DOI: doi:10.1038/s41586-022-04911-x ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dsrna (16 kDa, RNA from Drosophila melanogaster)
- Dicer2-loqspd-dsrna complex at its mid-translocation state (Complex from Drosophila melanogaster)
- Magnesium ion (24 Da, Ligand)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
dmDicer2-LoqsPD-dsRNA Active-dicing status
Resolution: 4.03 Å
EM Method: Single-particle
Fitted PDBs: 7w0e
Q-score: 0.366
Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J
Nature (2022) 607 pp. 399-406 [ Pubmed: 35768513 DOI: doi:10.1038/s41586-022-04911-x ]
- Dsrna (16 kDa, RNA from Drosophila melanogaster)
- Dicer2-loqspd-dsrna complex at its active-dicing state (Complex from Drosophila melanogaster)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
dmDicer2-LoqsPD-dsRNA Post-dicing status
Resolution: 4.55 Å
EM Method: Single-particle
Fitted PDBs: 7w0f
Q-score: 0.113
Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J
Nature (2022) 607 pp. 399-406 [ Pubmed: 35768513 DOI: doi:10.1038/s41586-022-04911-x ]
- Loquacious, isoform d (38 kDa, Protein from Drosophila melanogaster)
- Dicer2-loqspd-dsrna complex at its post-dicing state (Complex from Drosophila melanogaster)
- Dicer-2, isoform a (198 kDa, Protein from Drosophila melanogaster)
- Sirna (16 kDa, RNA from Drosophila melanogaster)
Structure of a membrane protein
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6lbh
Q-score: 0.461
Jin F, Sun M, Fujii T, Yamada Y, Wang J, Maturana AD, Wada M, Su S, Ma J, Takeda H, Kusakizako T, Tomita A, Nakada-Nakura Y, Liu K, Uemura T, Nomura Y, Nomura N, Ito K, Nureki O, Namba K, Iwata S, Yu Y, Hattori M
PLoS Biol (2021) 19 pp. e3001231-e3001231 [ Pubmed: 33905418 DOI: doi:10.1371/journal.pbio.3001231 ]
- Fab heavy chain (24 kDa, Protein from Mus musculus)
- Magnesium transporter mgte (19 kDa, Protein from Thermus thermophilus HB8)
- Fab light chain (23 kDa, Protein from Mus musculus)
- Mgte-fab complex (Complex from Thermus thermophilus)