› 6ypu

Electron Microscopy
2.9Å resolution

Acinetobacter baumannii ribosome-amikacin complex - 30S subunit body

Released:
DOI: 10.2210/pdb6ypu/pdb
PDB entry 6ypu coloured by chain, front view.
PDB entry 6ypu coloured by chain, side view.
PDB entry 6ypu coloured by chain, top view.
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Primary publication:
Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA
Structure 28 1087-1100.e3 (2020)
PMID: 32857965
Related structures: EMD-10869

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111916 (preferred)
Entry contents:
13 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (14 distinct):
Small ribosomal subunit protein uS2 Chain: c
Molecule details ›
Chain: c
Length: 250 amino acids
Theoretical weight: 27.68 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CC74 (Residues: 1-250; Coverage: 100%)
Gene names: HMPREF0010_02354, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS4 Chain: e
Molecule details ›
Chain: e
Length: 208 amino acids
Theoretical weight: 23.31 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD21 (Residues: 1-208; Coverage: 100%)
Gene names: HMPREF0010_02651, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: f
Molecule details ›
Chain: f
Length: 165 amino acids
Theoretical weight: 17.18 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD14 (Residues: 1-165; Coverage: 100%)
Gene names: HMPREF0010_02644, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: g
Molecule details ›
Chain: g
Length: 127 amino acids
Theoretical weight: 14.99 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C5Z0 (Residues: 1-127; Coverage: 100%)
Gene names: HMPREF0010_00170, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS8 Chain: i
Molecule details ›
Chain: i
Length: 131 amino acids
Theoretical weight: 14.25 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD11 (Residues: 1-131; Coverage: 100%)
Gene names: HMPREF0010_02641, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS11 Chain: l
Molecule details ›
Chain: l
Length: 128 amino acids
Theoretical weight: 13.56 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD20 (Residues: 1-128; Coverage: 100%)
Gene names: HMPREF0010_02650, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: m
Molecule details ›
Chain: m
Length: 124 amino acids
Theoretical weight: 13.8 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C9P6 (Residues: 1-124; Coverage: 100%)
Gene names: HMPREF0010_01359, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS15 Chain: p
Molecule details ›
Chain: p
Length: 89 amino acids
Theoretical weight: 10.15 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CAU9 (Residues: 1-89; Coverage: 100%)
Gene names: HMPREF0010_01879, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: q
Molecule details ›
Chain: q
Length: 83 amino acids
Theoretical weight: 9.22 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CCR5 (Residues: 1-83; Coverage: 100%)
Gene names: HMPREF0010_02545, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: r
Molecule details ›
Chain: r
Length: 85 amino acids
Theoretical weight: 9.54 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD06 (Residues: 1-85; Coverage: 100%)
Gene names: HMPREF0010_02636, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: s
Molecule details ›
Chain: s
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C5Y9 (Residues: 1-75; Coverage: 100%)
Gene names: HMPREF0010_00169, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS20 Chain: u
Molecule details ›
Chain: u
Length: 88 amino acids
Theoretical weight: 9.72 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C7N1 (Residues: 1-88; Coverage: 100%)
Gene names: HMPREF0010_00761, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: v
Molecule details ›
Chain: v
Length: 71 amino acids
Theoretical weight: 8.47 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C5Q3 (Residues: 1-71; Coverage: 100%)
Gene names: HMPREF0010_00083, rpsU
Sequence domains: Ribosomal protein S21
16S ribosomal RNA Chains: 2, 4
Molecule details ›
Chains: 2, 4
Length: 1544 nucleotides
Theoretical weight: 500.13 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 59 x MG
Ligand AKN 1 x AKN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-10869

Quick links

Citations

1 review citation

Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation.
Jeremia et al. (2023)
5 other articles

2 mentions without citation

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Nicholson et al. (2020)
1 more