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author:"Fraser JS" AND current_status:"REL" AND xref_links:"pdbekb"
Release date: Nov. 15, 2023
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8tu6
Q-score: 0.525
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8tu6
Q-score: 0.525
Varkaris A, Pazolli E, Gunaydin H, Wang Q, Pierce L, Boezio AA, Bulku A, DiPietro L, Fridrich C, Frost A, Giordanetto F, Hamilton EP, Harris K, Holliday M, Hunter TL, Iskandar A, Ji Y, Larivee A, LaRochelle JR, Lescarbeau A, Llambi F, Lormil B, Mader MM, Mar BG, Martin I, McLean TH, Michelsen K, Pechersky Y, Puente-Poushnejad E, Raynor K, Rogala D, Samadani R, Schram AM, Shortsleeves K, Swaminathan S, Tajmir S, Tan G, Tang Y, Valverde R, Wehrenberg B, Wilbur J, Williams BR, Zeng H, Zhang H, Walters WP, Wolf BB, Shaw DE, Bergstrom DA, Watters J, Fraser JS, Fortin PD, Kipp DR
Cancer Discov (2024) 14 pp. 240-257 [ Pubmed: 37916956 DOI: doi:10.1158/2159-8290.CD-23-0944 ]
Sample:
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (126 kDa, Protein from Homo sapiens)
- Phosphatidylinositol 3-kinase regulatory subunit alpha (83 kDa, Protein from Homo sapiens)
- P85 (Complex from Homo sapiens)
- Pi3kalpha (850 kDa, Complex from Homo sapiens)
- P110 (Complex from Homo sapiens)
E. coli 50S ribosome bound to compound streptogramin A analog 3142
Release date: June 28, 2023
Resolution: 1.91 Å
EM Method: Single-particle
Fitted PDBs: 8e30
Q-score: 0.629
Resolution: 1.91 Å
EM Method: Single-particle
Fitted PDBs: 8e30
Q-score: 0.629
Li Q, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 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)
- N-{2-[4-(aminomethyl)-1h-1,2,3-triazol-1-yl]ethyl}-2-[(3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-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-4-yl]acetamide (698 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound streptogramin analogs SA1 and SB1
Release date: June 28, 2023
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8e32
Q-score: 0.609
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8e32
Q-score: 0.609
Takahashi Y, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- (3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-yn-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 (555 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- ~{n}-[(3~{s},6~{s},12~{r},15~{s},16~{r},19~{s},22~{s},24~{r})-12-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethyl]-4,16-dimethyl-24-oxidanyl-2,5,11,14,18,21-hexakis(oxidanylidene)-19-phenyl-3-(phenylmethyl)-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide (867 Da, Ligand)
E. coli 50S ribosome bound to compound streptogramin analog SAB001
Release date: June 28, 2023
Resolution: 2.23 Å
EM Method: Single-particle
Fitted PDBs: 8e33
Q-score: 0.602
Resolution: 2.23 Å
EM Method: Single-particle
Fitted PDBs: 8e33
Q-score: 0.602
Takahashi Y, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- N-{(4r,6r,9s,10r,13s,15as,17r,20r,22s,24as)-22-benzyl-6-[2-(4-{[(3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-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-4-yl]methyl}-1h-1,2,3-triazol-1-yl)ethyl]-17-hydroxy-10,23-dimethyl-5,8,12,15,21,24-hexaoxo-13-phenyldocosahydro-12h-pyrido[2,1-f]pyrrolo[2,1-l][1,4,7,10,13,16]oxapentaazacyclononadecin-9-yl}-3-hydroxypyridine-2-carboxamide (1 kDa, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound SAB002
Release date: June 28, 2023
Resolution: 2.27 Å
EM Method: Single-particle
Fitted PDBs: 8e35
Q-score: 0.569
Resolution: 2.27 Å
EM Method: Single-particle
Fitted PDBs: 8e35
Q-score: 0.569
Takahashi Y, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- N-{(4r,6r,9s,10r,13s,15as,17r,20r,22s,24as)-22-benzyl-6-[3-(4-{[(3r,4r,5e,10e,12e,14s,16r,23r,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-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-4-yl]methyl}-1h-1,2,3-triazol-1-yl)propyl]-17-hydroxy-10,23-dimethyl-5,8,12,15,21,24-hexaoxo-13-phenyldocosahydro-12h-pyrido[2,1-f]pyrrolo[2,1-l][1,4,7,10,13,16]oxapentaazacyclononadecin-9-yl}-3-hydroxypyridine-2-carboxamide (1 kDa, Ligand)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound streptogramin A analog 3146
Release date: June 28, 2023
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8e36
Q-score: 0.57
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8e36
Q-score: 0.57
Li Q, Pellegrino J, Lee DJ, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 2-[(3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-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-4-yl]-n-{2-[4-(pyridin-4-yl)-1h-1,2,3-triazol-1-yl]ethyl}acetamide (746 Da, Ligand)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 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)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to D-linker solithromycin conjugate
Release date: June 28, 2023
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8e3l
Q-score: 0.601
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8e3l
Q-score: 0.601
Boyce JH, Pellegrino J, Lee DJ, Ecker AK, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- (2~{r})-~{n}-[(2~{r})-6-azanyl-1-[[(2~{r})-1-[[(2~{r})-1-[[3-[1-[4-[(1~{s},2~{r},5~{s},7~{r},8~{r},9~{r},11~{r},13~{r},14~{r})-8-[(2~{s},3~{r},4~{s},6~{r})-4-(dimethylamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-2-ethyl-5-fluoranyl-9-methoxy-1,5,7,11,13-pentamethyl-4,6,12,16-tetrakis(oxidanylidene)-3,17-dioxa-15-azabicyclo[12.3.0]heptadecan-15-yl]butyl]-1,2,3-triazol-4-yl]phenyl]amino]-4-methylsulfanyl-1-oxidanylidene-butan-2-yl]amino]-3-(4-hydroxyphenyl)-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-hexan-2-yl]-1-[(2~{r})-2-[[(2~{r})-2-[2-[[2,3-bis(oxidanyl)phenyl]carbonyl-[4-[[2,3-bis(oxidanyl)phenyl]carbonylamino]butyl]amino]ethanoylamino]-3-(1~{h}-indol-3-yl)propanoyl]amino]-3-oxidanyl-propanoyl]pyrrolidine-2-carboxamide (2 kDa, Ligand)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 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)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal rna (941 kDa, RNA from Escherichia coli)
E. coli 50S ribosome bound to L-linker solithromycin conjugate
Release date: June 28, 2023
Resolution: 2.25 Å
EM Method: Single-particle
Fitted PDBs: 8e3m
Q-score: 0.604
Resolution: 2.25 Å
EM Method: Single-particle
Fitted PDBs: 8e3m
Q-score: 0.604
Boyce JH, Pellegrino J, Lee DJ, Ecker AK, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- N-acetyl-l-tyrosyl-n-[(3m)-3-(1-{4-[(3as,4r,7s,9r,10r,11r,13r,15r,15ar)-4-ethyl-7-fluoro-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-d-xylo-hexopyranosyl]oxy}dodecahydro-2h-oxacyclotetradecino[4,3-d][1,3]oxazol-1(4h)-yl]butyl}-1h-1,2,3-triazol-4-yl)phenyl]-l-methioninamide (1 kDa, Ligand)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to solithromycin and VM1
Release date: June 28, 2023
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 8e3o
Q-score: 0.618
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 8e3o
Q-score: 0.618
Boyce JH, Pellegrino J, Lee DJ, Ecker AK, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Virginiamycin m1 (525 Da, Ligand)
- (3as,4r,7s,9r,10r,11r,13r,15r,15ar)-1-{4-[4-(3-aminophenyl)-1h-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2h-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-d-xylo-hexopyranoside (845 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to tiamulin and VS1
Release date: June 28, 2023
Resolution: 2.13 Å
EM Method: Single-particle
Fitted PDBs: 8e41
Q-score: 0.611
Resolution: 2.13 Å
EM Method: Single-particle
Fitted PDBs: 8e41
Q-score: 0.611
Edmonson Q, Pellegrino J, Lee DJ, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal rna (941 kDa, RNA from Escherichia coli)
- Tiamulin (493 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- Virginiamycin s1 (841 Da, Protein from Streptomyces virginiae)