› 8ev6

X-ray diffraction
2.95Å resolution

Crystal structure of the Thermus thermophilus 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs

Released:
DOI: 10.2210/pdb8ev6/pdb
Model geometry
Fit model/data
PDB entry 8ev6 coloured by chain, front view.
PDB entry 8ev6 coloured by chain, side view.
PDB entry 8ev6 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG
OpenAccess logo Nat Commun 14 4666 (2023)
PMID: 37537169

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-225149 (preferred)
Entry contents:
49 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (55 distinct):
Large ribosomal subunit protein uL2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: 1F, 2F
Large ribosomal subunit protein uL5 Chains: 1G, 2G
Large ribosomal subunit protein uL6 Chains: 1H, 2H
Large ribosomal subunit protein bL9 Chains: 1I, 2I
Large ribosomal subunit protein uL13 Chains: 1N, 2N
Large ribosomal subunit protein uL14 Chains: 1O, 2O
Large ribosomal subunit protein uL15 Chains: 1P, 2P
Large ribosomal subunit protein uL16 Chains: 1Q, 2Q
Large ribosomal subunit protein bL17 Chains: 1R, 2R
Large ribosomal subunit protein uL18 Chains: 1S, 2S
Large ribosomal subunit protein bL19 Chains: 1T, 2T
Large ribosomal subunit protein bL20 Chains: 1U, 2U
Large ribosomal subunit protein bL21 Chains: 1V, 2V
Large ribosomal subunit protein uL22 Chains: 1W, 2W
Large ribosomal subunit protein uL23 Chains: 1X, 2X
Large ribosomal subunit protein uL24 Chains: 1Y, 2Y
Large ribosomal subunit protein bL25 Chains: 1Z, 2Z
Large ribosomal subunit protein bL27 Chains: 10, 20
Large ribosomal subunit protein bL28 Chains: 11, 21
Large ribosomal subunit protein uL29 Chains: 12, 22
Large ribosomal subunit protein uL30 Chains: 13, 23
Large ribosomal subunit protein bL31 Chains: 14, 24
Large ribosomal subunit protein bL32 Chains: 15, 25
Large ribosomal subunit protein bL33 Chains: 16, 26
Large ribosomal subunit protein bL34 Chains: 17, 27
Large ribosomal subunit protein bL35 Chains: 18, 28
Large ribosomal subunit protein bL36 Chains: 19, 29
Small ribosomal subunit protein uS2 Chains: 1b, 2b
Small ribosomal subunit protein uS3 Chains: 1c, 2c
Small ribosomal subunit protein uS4 Chains: 1d, 2d
Small ribosomal subunit protein uS5 Chains: 1e, 2e
Small ribosomal subunit protein bS6 Chains: 1f, 2f
Small ribosomal subunit protein uS7 Chains: 1g, 2g
Small ribosomal subunit protein uS8 Chains: 1h, 2h
Small ribosomal subunit protein uS9 Chains: 1i, 2i
Small ribosomal subunit protein uS10 Chains: 1j, 2j
Small ribosomal subunit protein uS11 Chains: 1k, 2k
Small ribosomal subunit protein uS12 Chains: 1l, 2l
Small ribosomal subunit protein uS13 Chains: 1m, 2m
Small ribosomal subunit protein uS14 Chains: 1n, 2n
Small ribosomal subunit protein uS15 Chains: 1o, 2o
Small ribosomal subunit protein bS16 Chains: 1p, 2p
Small ribosomal subunit protein uS17 Chains: 1q, 2q
Small ribosomal subunit protein bS18 Chains: 1r, 2r
Small ribosomal subunit protein uS19 Chains: 1s, 2s
Small ribosomal subunit protein bS20 Chains: 1t, 2t
Small ribosomal subunit protein bTHX Chains: 1u, 2u
23S ribosomal RNA Chains: 1A, 2A
5S ribosomal RNA Chains: 1B, 2B
16S ribosomal RNA Chains: 1a, 2a
Messenger RNA Chains: 1v, 2v
A-site and E-site tRNAs Chains: 1w, 1y, 2w, 2y
P-site tRNA Chains: 1x, 2x

Ligands and Environments

4 bound ligands:
Ligand MG 2333 x MG
Ligand AKN 8 x AKN
Ligand ZN 12 x ZN
Ligand SF4 2 x SF4
15 modified residues:
Ligand PSU 22 x PSU
Ligand 5MU 10 x 5MU
Ligand 4OC 4 x 4OC
Ligand 5MC 14 x 5MC
Ligand OMG 2 x OMG
Ligand 2MA 2 x 2MA
Ligand 2MU 2 x 2MU
Ligand 7MG 6 x 7MG
Ligand M2G 2 x M2G
Ligand 2MG 2 x 2MG
Ligand UR3 2 x UR3
Ligand MA6 4 x MA6
Ligand 0TD 2 x 0TD
Ligand 4SU 6 x 4SU
Ligand MIA 4 x MIA

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 210.148Å b: 446.822Å c: 620.282Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.223 0.272

Quick links

Citations

2 review citations

Mechanistic Insights into Clinically Relevant Ribosome-Targeting Antibiotics.
Krawczyk et al. (2024)
1 more