Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with P-tRNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nso
Q-score: 0.551
Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmuller H, Mankin AS, Innis CA, Vazquez-Laslop N, Wilson DN
Nat Commun (2021) 12 pp. 4466-4466 [ Pubmed: 34294725 DOI: doi:10.1038/s41467-021-24674-9 ]
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- Erythromycin a (733 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Ptrna-leu (28 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 16s rrna (1540-mer) (499 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- Structure of ermdl-erythromycin-stalled 70s e. coli ribosomal complex with p-trna (Complex from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 23s rrna (2903-mer) (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- Ermdl (877 Da, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Mrna (872 Da, RNA from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5njt
Q-score: 0.381
Beckert B, Abdelshahid M, Schafer H, Steinchen W, Arenz S, Berninghausen O, Beckmann R, Bange G, Turgay K, Wilson DN
EMBO J (2017) 36 pp. 2061-2072 [ Pubmed: 28468753 DOI: doi:10.15252/embj.201696189 ]
- 50s ribosomal protein l27 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Structure of the bacillus subtilis hibernating 100s ribosome reveals the basis for 70s dimerization (Complex from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 16s ribosomal rna (500 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s11 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s3 (23 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l10 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Ribosome hibernation promotion factor (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 5s ribosomal rna (36 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l16 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l24 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 23s ribosomal rna (947 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s13 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s2 (25 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s19 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- 50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 5mlc
Q-score: 0.39
Graf M, Arenz S, Huter P, Donhofer A, Novacek J, Wilson DN
Nucleic Acids Res (2017) 45 pp. 2887-2896 [ Pubmed: 27986857 DOI: doi:10.1093/nar/gkw1272 ]
- 4.8s ribosomal rna, chloroplastic (33 kDa, RNA from Spinacia oleracea)
- 23s ribosomal rna, chloroplastic (911 kDa, RNA from Spinacia oleracea)
- 5s ribosomal rna, chloroplastic (39 kDa, RNA from Spinacia oleracea)
- 50s ribosomal protein l32, chloroplastic (6 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l34, chloroplastic (16 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l2, chloroplastic (29 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l5, chloroplastic (24 kDa, Protein from Spinacia oleracea)
- Ribosome-recycling factor, chloroplastic (30 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l27, chloroplastic (21 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l22, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l35, chloroplastic (17 kDa, Protein from Spinacia oleracea)
- 50s subunit of the spinach chloroplast ribosome (Complex from Spinacia oleracea)
- 50s ribosomal protein l17, chloroplastic (14 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l16, chloroplastic (15 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l15, chloroplastic (29 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l36, chloroplastic (4 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l18, chloroplastic (18 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l14, chloroplastic (13 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l29, chloroplastic (19 kDa, Protein from Spinacia oleracea)
- Psrp6, chloroplastic (12 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l24, chloroplastic (21 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l20, chloroplastic (15 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l4, chloroplastic (32 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l21, chloroplastic (28 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l9, chloroplastic (22 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l28, chloroplastic (16 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l33, chloroplastic (7 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l6, chloroplastic (24 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l3, chloroplastic (33 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l19, chloroplastic (26 kDa, Protein from Spinacia oleracea)
- Psrp5alpha, chloroplastic (15 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l23, chloroplastic (21 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l13, chloroplastic (28 kDa, Protein from Spinacia oleracea)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 5kcr
Q-score: 0.346
Arenz S, Juette MF, Graf M, Nguyen F, Huter P, Polikanov YS, Blanchard SC, Wilson DN
PNAS (2016) 113 pp. 7527-7532 [ Pubmed: 27330110 DOI: doi:10.1073/pnas.1604790113 ]
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 16s ribosomal rna (498 kDa, RNA from Escherichia coli (strain K12))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- Cryo-em structure of the escherichia coli 70s ribosome in complex with antibiotic avilamycin a, mrna and p-site trna at 3.6a resolution (Complex from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- P-site trna (28 kDa, RNA from Escherichia coli (strain K12))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
- Mrna (2 kDa, RNA from Synthetic)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- (2r,3s,4r,6s)-4-hydroxy-6-{[(2r,3ar,4r,4'r,5's,6s,6'r,7ar)-4'-hydroxy-6-{[(2s,3r,4r,5s,6r)-3-hydroxy-2-{[(2r,3s,4s,5s,6s)-4-hydroxy-6-({(2r,3as,3a'r,6s,6'r,7r,7'r,7ar,7a'r)-7'-hydroxy-7'-[(1s)-1-hydroxyethyl]-6'-methyl-7-[(2-methylpropanoyl)oxy]octahydro-4h-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}oxy)-5-methoxy-2-(methoxymethyl)tetrahydro-2h-pyran-3-yl]oxy}-5-methoxy-6-methyltetrahydro-2h-pyran-4-yl]oxy}-4,6',7a-trimethyloctahydro-4h-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-2-methyltetrahydro-2h-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name) (1 kDa, Ligand)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))