Structure of R2 with 3'UTR and DNA in binding state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ibw
Q-score: 0.385
Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG
Cell (2023) 186 pp. 2865-2879.e20 [ DOI: doi:10.1016/j.cell.2023.05.032 Pubmed: 37301196 ]
- Zinc ion (65 Da, Ligand)
- Reverse transcriptase-like protein (123 kDa, Protein from Bombyx mori)
- 3'utr (16 kDa, RNA from Bombyx mori)
- Dna (60-mer) (18 kDa, DNA from Bombyx mori)
- R2 complex (177 kDa, Complex from Bombyx mori)
- Dna (60-mer) (18 kDa, DNA from Bombyx mori)
Structure of R2 with 3'UTR and DNA in unwinding state
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 8ibx
Q-score: 0.385
Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG
Cell (2023) 186 pp. 2865-2879.e20 [ DOI: doi:10.1016/j.cell.2023.05.032 Pubmed: 37301196 ]
- Zinc ion (65 Da, Ligand)
- Reverse transcriptase-like protein (123 kDa, Protein from Bombyx mori)
- 3'utr (16 kDa, RNA from Bombyx mori)
- Dna (60-mer) (18 kDa, DNA from Bombyx mori)
- R2 complex (177 kDa, Complex from Bombyx mori)
- Dna (60-mer) (18 kDa, DNA from Bombyx mori)
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8iby
Q-score: 0.342
Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG
Cell (2023) 186 pp. 2865-2879.e20 [ DOI: doi:10.1016/j.cell.2023.05.032 Pubmed: 37301196 ]
- 5'orf rna (72 kDa, RNA from Bombyx mori)
- Zinc ion (65 Da, Ligand)
- Reverse transcriptase-like protein (123 kDa, Protein from Bombyx mori)
- R2 complex (177 kDa, Complex from Bombyx mori)
Structure of R2 with 5'ORF and 3'UTR
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8ibz
Q-score: 0.435
Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG
Cell (2023) 186 pp. 2865-2879.e20 [ DOI: doi:10.1016/j.cell.2023.05.032 Pubmed: 37301196 ]
- 5orf-linker-3utr (65 kDa, RNA from Bombyx mori)
- Zinc ion (65 Da, Ligand)
- Reverse transcriptase-like protein (123 kDa, Protein from Bombyx mori)
- R2 complex (177 kDa, Complex from Bombyx mori)
CalA3 complex structure with amidation product
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 8i4y
Q-score: 0.416
Wang J, Wang X, Li X, Kong L, Du Z, Li D, Gou L, Wu H, Cao W, Wang X, Lin S, Shi T, Deng Z, Wang Z, Liang J
Nat Commun (2023) 14 pp. 1319-1319 [ Pubmed: 36899013 DOI: doi:10.1038/s41467-023-36989-w ]
- 3-hydroxyanthranilic acid (153 Da, Ligand)
- An assembly-line polyketide synthase module containing ks-at-dh-kr domains with amidation product (360 kDa, Cellular component from Streptomyces chartreusis NRRL 3882cha)
- Beta-ketoacyl-acyl-carrier-protein synthase i (178 kDa, Protein from Streptomyces chartreusis NRRL 3882)
- 11-oxidanylidene-11-(1~{h}-pyrrol-2-yl)undecanoic acid (265 Da, Ligand)
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state1)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7yr2
Q-score: 0.354
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ Pubmed: 36270286 DOI: doi:10.1016/j.chom.2022.09.018 ]
- Ba.2.75 s trimer in complex with ace2 (Complex from Homo sapiens)
- Ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Ba.2.75 s trimer (Complex)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state2)
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 7yr3
Q-score: 0.314
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ Pubmed: 36270286 DOI: doi:10.1016/j.chom.2022.09.018 ]
- Zinc ion (65 Da, Ligand)
- Ba.2.75 spike trimer (Complex from Homo sapiens)
- Ba.2.75 spike trimer in complex with ace2 (state2) (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ace2 (Complex)
- Chloride ion (35 Da, Ligand)
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)