Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6yhs
Q-score: 0.639
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA
Structure (2020) 28 pp. 1087-1100.e3 [ DOI: doi:10.1016/j.str.2020.08.004 Pubmed: 32857965 ]
- 50s ribosomal protein l36 (4 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l13 (15 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l22 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l32 (7 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l28 (9 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l33 (6 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l15 (15 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l18 (12 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l24 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l35 (7 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l3 (22 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l14 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l23 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l17 (14 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l27 (9 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l20 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l2 (30 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l4 (21 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l5 (20 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l19 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l21 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l34 (5 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l16 (15 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Acinetobacter baumannii ribosome-amikacin complex - 50s subunit (Complex from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- E-site trna (24 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l6 (19 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l30 (6 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l29 (7 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 23s ribosomal rna (940 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 5s ribosomal rna (37 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l25 (10 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
Acinetobacter baumannii ribosome-amikacin complex - 30S subunit body
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6ypu
Q-score: 0.611
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA
Structure (2020) 28 pp. 1087-1100.e3 [ DOI: doi:10.1016/j.str.2020.08.004 Pubmed: 32857965 ]
- 30s ribosomal protein s4 (23 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- Acinetobacter baumannii ribosome-amikacin complex - 30s subunit body (Complex from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s11 (13 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s20 (9 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s8 (14 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s12 (13 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s2 (27 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s17 (9 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s21 (8 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 16s ribosomal rna (500 kDa, RNA from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s18 (9 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s5 (17 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s16 (9 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s6 (14 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- (2s)-n-[(1r,2s,3s,4r,5s)-4-[(2r,3r,4s,5s,6r)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2s,3r,4s,5s ,6r)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide (585 Da, Ligand)
- 30s ribosomal protein s15 (10 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6ys5
Q-score: 0.597
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA
Structure (2020) 28 pp. 1087-1100.e3 [ DOI: doi:10.1016/j.str.2020.08.004 Pubmed: 32857965 ]
- E-site trna (24 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s13 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Magnesium ion (24 Da, Ligand)
- Acinetobacter baumannii ribosome-amikacin complex - 30s subunit head (Complex from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s14 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s3 (27 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Mrna (1 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 16s ribosomal rna (500 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s19 (10 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s7 (17 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s10 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 30s ribosomal protein s9 (14 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6ysi
Q-score: 0.653
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA
Structure (2020) 28 pp. 1087-1100.e3 [ DOI: doi:10.1016/j.str.2020.08.004 Pubmed: 32857965 ]
- 50s ribosomal protein l36 (4 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l13 (15 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l22 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l32 (7 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l28 (9 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l33 (6 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l31 (8 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l15 (15 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l18 (12 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l24 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l35 (7 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l3 (22 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l14 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l23 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l17 (14 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l27 (9 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l20 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l2 (30 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l4 (21 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l5 (20 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l19 (13 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l21 (11 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l34 (5 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l16 (15 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l6 (19 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- E-site trna (24 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l30 (6 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l29 (7 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- Tigecycline (587 Da, Ligand)
- Acinetobacter baumannii ribosome-tigecycline complex - 50s subunit (Complex from Acinetobacter baumannii)
- 23s ribosomal rna (940 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 5s ribosomal rna (37 kDa, RNA from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 50s ribosomal protein l25 (10 kDa, Protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6ytf
Q-score: 0.511
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA
Structure (2020) 28 pp. 1087-1100.e3 [ Pubmed: 32857965 DOI: doi:10.1016/j.str.2020.08.004 ]
- Acinetobacter baumannii ribosome-tigecycline complex - 30s subunit head (Complex from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841)
- 16s ribosomal rna (500 kDa, RNA from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s3 (27 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s13 (13 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- Magnesium ion (24 Da, Ligand)
- Tigecycline (587 Da, Ligand)
- 30s ribosomal protein s14 (11 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s7 (17 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- Mrna (1 kDa, RNA from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s10 (11 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s19 (10 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- E-site trna (24 kDa, RNA from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
- 30s ribosomal protein s9 (14 kDa, Protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))