› 6ytf

Electron Microscopy
3Å resolution

Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head

Released:
DOI: 10.2210/pdb6ytf/pdb
PDB entry 6ytf coloured by chain, front view.
PDB entry 6ytf coloured by chain, side view.
PDB entry 6ytf 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-10915

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111930 (preferred)
Entry contents:
7 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (10 distinct):
Small ribosomal subunit protein uS3 Chain: d
Molecule details ›
Chain: d
Length: 250 amino acids
Theoretical weight: 27.97 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD03 (Residues: 1-250; Coverage: 100%)
Gene names: HMPREF0010_02633, rpsC
Sequence domains:
Small ribosomal subunit protein uS7 Chain: h
Molecule details ›
Chain: h
Length: 156 amino acids
Theoretical weight: 17.73 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C9P7 (Residues: 1-156; Coverage: 100%)
Gene names: HMPREF0010_01360, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9 Chain: j
Molecule details ›
Chain: j
Length: 128 amino acids
Theoretical weight: 14.29 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CG36 (Residues: 1-128; Coverage: 100%)
Gene names: HMPREF0010_03716, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: k
Molecule details ›
Chain: k
Length: 103 amino acids
Theoretical weight: 11.72 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CCZ6 (Residues: 6-108; Coverage: 95%)
Gene names: HMPREF0010_02626, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS13 Chain: n
Molecule details ›
Chain: n
Length: 118 amino acids
Theoretical weight: 13.3 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD19 (Residues: 1-118; Coverage: 100%)
Gene names: HMPREF0010_02649, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: o
Molecule details ›
Chain: o
Length: 101 amino acids
Theoretical weight: 11.44 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD10 (Residues: 1-101; Coverage: 100%)
Gene names: HMPREF0010_02640, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS19 Chain: t
Molecule details ›
Chain: t
Length: 91 amino acids
Theoretical weight: 10.21 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD01 (Residues: 1-91; Coverage: 100%)
Gene names: HMPREF0010_02631, rpsS
Sequence domains: Ribosomal protein S19
16S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 1544 nucleotides
Theoretical weight: 500.13 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
E-site tRNA Chain: 7
Molecule details ›
Chain: 7
Length: 77 nucleotides
Theoretical weight: 24.82 KDa
Sequence domains: tRNA
Messenger RNA Chain: 9
Molecule details ›
Chain: 9
Length: 4 nucleotides
Theoretical weight: 1.18 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 24 x MG
Ligand T1C 1 x T1C
4 modified residues:
Ligand 4SU 1 x 4SU
Ligand H2U 1 x H2U
Ligand 5MU 1 x 5MU
Ligand PSU 1 x PSU

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-10915

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