SARS-CoV-2 Spike bound to mNb6 in closed conformation
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 7kkl
Q-score: 0.514
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbolle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, Garcia-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A
Science (2020) 370 pp. 1473-1479 [ Pubmed: 33154106 DOI: doi:10.1126/science.abe3255 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Synthetic nanobody mnb6 (13 kDa, Protein from synthetic construct)
- Complex of spike s2p glycoprotein with synthetic nanobody mnb6 (Complex)
- Synthetic nanobody mnb6 (Complex from synthetic construct)
- Spike s2p glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
E. coli 50S ribosome bound to compounds 46 and VS1
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6pc5
Q-score: 0.557
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- (2r)-2-[(3s,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-4,12-dimethyl-1,7,22-trioxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate (717 Da, Ligand)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Virginiamycin s1 (841 Da, Protein from Streptomyces virginiae)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 47
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6pc6
Q-score: 0.563
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- (3r,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,7h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione (557 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 46
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6pc7
Q-score: 0.552
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- (2r)-2-[(3s,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-4,12-dimethyl-1,7,22-trioxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate (717 Da, Ligand)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 40q
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6pc8
Q-score: 0.513
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- (2r)-2-[(3s,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-1,7,16,22-tetraoxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate (713 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 21
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6pch
Q-score: 0.488
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- (3r,4r,5e,10e,12e,14s,26ar)-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-8,9,14,15,24,25,26,26a-octahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,16,22(4h,17h)-tetrone (553 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to VM2
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 6pcq
Q-score: 0.532
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- (3r,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-3-(propan-2-yl)-8,9,14,15,24,25,26,26a-octahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,16,22(4h,17h)-tetrone (527 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 40o
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6pcr
Q-score: 0.567
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- (2r)-2-[(3s,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-1,7,16,22-tetraoxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl (2-bromopyridin-4-yl)carbamate (742 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 40e
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 6pcs
Q-score: 0.525
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- (2r)-2-[(3s,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-1,7,16,22-tetraoxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl [4-(trifluoromethyl)phenyl]carbamate (730 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound 41q
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 6pct
Q-score: 0.552
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB
Nature (2020) 586 pp. 145-150 [ Pubmed: 32968273 DOI: doi:10.1038/s41586-020-2761-3 ]
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- (2s)-2-[(3s,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-1,7,16,22-tetraoxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate (713 Da, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)