› 6yhs

Electron Microscopy
2.7Å resolution

Acinetobacter baumannii ribosome-amikacin complex - 50S subunit

Released:
DOI: 10.2210/pdb6yhs/pdb
PDB entry 6yhs coloured by chain, front view.
PDB entry 6yhs coloured by chain, side view.
PDB entry 6yhs 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-10809

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111924 (preferred)
Entry contents:
27 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 30.32 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD00 (Residues: 1-274; Coverage: 100%)
Gene names: HMPREF0010_02630, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 212 amino acids
Theoretical weight: 22.51 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CCZ7 (Residues: 3-214; Coverage: 99%)
Gene names: HMPREF0010_02627, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 200 amino acids
Theoretical weight: 21.58 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CCZ8 (Residues: 1-200; Coverage: 100%)
Gene names: HMPREF0010_02628, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: D
Molecule details ›
Chain: D
Length: 178 amino acids
Theoretical weight: 20.05 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD09 (Residues: 1-178; Coverage: 100%)
Gene names: HMPREF0010_02639, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: E
Molecule details ›
Chain: E
Length: 177 amino acids
Theoretical weight: 19.13 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD12 (Residues: 1-177; Coverage: 100%)
Gene names: HMPREF0010_02642, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: F
Molecule details ›
Chain: F
Length: 142 amino acids
Theoretical weight: 15.95 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CG35 (Residues: 1-142; Coverage: 100%)
Gene names: HMPREF0010_03715, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: G
Molecule details ›
Chain: G
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD07 (Residues: 1-122; Coverage: 100%)
Gene names: HMPREF0010_02637, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 15.51 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD16 (Residues: 1-146; Coverage: 100%)
Gene names: HMPREF0010_02646, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: I
Molecule details ›
Chain: I
Length: 137 amino acids
Theoretical weight: 15.5 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD04 (Residues: 1-137; Coverage: 100%)
Gene names: HMPREF0010_02634, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: J
Molecule details ›
Chain: J
Length: 125 amino acids
Theoretical weight: 14.02 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD23 (Residues: 1-125; Coverage: 100%)
Gene names: HMPREF0010_02653, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: K
Molecule details ›
Chain: K
Length: 116 amino acids
Theoretical weight: 12.44 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD13 (Residues: 1-116; Coverage: 100%)
Gene names: HMPREF0010_02643, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: L
Molecule details ›
Chain: L
Length: 122 amino acids
Theoretical weight: 13.62 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CCR8 (Residues: 1-122; Coverage: 100%)
Gene names: HMPREF0010_02548, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: M
Molecule details ›
Chain: M
Length: 119 amino acids
Theoretical weight: 13.47 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CA76 (Residues: 1-119; Coverage: 100%)
Gene names: HMPREF0010_01656, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: N
Molecule details ›
Chain: N
Length: 103 amino acids
Theoretical weight: 11.5 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CDQ6 (Residues: 1-103; Coverage: 100%)
Gene names: HMPREF0010_02886, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: O
Molecule details ›
Chain: O
Length: 110 amino acids
Theoretical weight: 11.96 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD02 (Residues: 1-110; Coverage: 100%)
Gene names: HMPREF0010_02632, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: P
Molecule details ›
Chain: P
Length: 106 amino acids
Theoretical weight: 11.61 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CCZ9 (Residues: 1-106; Coverage: 100%)
Gene names: HMPREF0010_02629, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: Q
Molecule details ›
Chain: Q
Length: 105 amino acids
Theoretical weight: 11.19 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD08 (Residues: 1-105; Coverage: 100%)
Gene names: HMPREF0010_02638, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: R
Molecule details ›
Chain: R
Length: 98 amino acids
Theoretical weight: 10.91 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C9L7 (Residues: 6-103; Coverage: 95%)
Gene names: HMPREF0010_01330, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: S
Molecule details ›
Chain: S
Length: 85 amino acids
Theoretical weight: 9.07 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CDQ7 (Residues: 1-85; Coverage: 100%)
Gene names: HMPREF0010_02887, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: T
Molecule details ›
Chain: T
Length: 78 amino acids
Theoretical weight: 9.13 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CAL0 (Residues: 1-78; Coverage: 100%)
Gene names: HMPREF0010_01790, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: U
Molecule details ›
Chain: U
Length: 65 amino acids
Theoretical weight: 7.45 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD05 (Residues: 1-65; Coverage: 100%)
Gene names: HMPREF0010_02635, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: V
Molecule details ›
Chain: V
Length: 58 amino acids
Theoretical weight: 6.65 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD15 (Residues: 1-58; Coverage: 100%)
Gene names: HMPREF0010_02645, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: X
Molecule details ›
Chain: X
Length: 61 amino acids
Theoretical weight: 7.1 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0C9K5 (Residues: 1-61; Coverage: 100%)
Gene names: HMPREF0010_01318, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: Y
Molecule details ›
Chain: Y
Length: 51 amino acids
Theoretical weight: 6.11 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CAL1 (Residues: 1-51; Coverage: 100%)
Gene names: HMPREF0010_01791, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: Z
Molecule details ›
Chain: Z
Length: 44 amino acids
Theoretical weight: 5.19 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CG06 (Residues: 19-62; Coverage: 71%)
Gene names: HMPREF0010_03686, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: a
Molecule details ›
Chain: a
Length: 64 amino acids
Theoretical weight: 7.42 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CA77 (Residues: 1-64; Coverage: 100%)
Gene names: HMPREF0010_01657, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: b
Molecule details ›
Chain: b
Length: 38 amino acids
Theoretical weight: 4.28 KDa
Source organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
UniProt:
  • Canonical: D0CD18 (Residues: 1-38; Coverage: 100%)
Gene names: HMPREF0010_02648, rpmJ
Sequence domains: Ribosomal protein L36
23S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 2903 nucleotides
Theoretical weight: 940.33 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 117 nucleotides
Theoretical weight: 37.61 KDa
Sequence domains: 5S ribosomal RNA
E-site tRNA Chains: 6, 8
Molecule details ›
Chains: 6, 8
Length: 77 nucleotides
Theoretical weight: 24.35 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 160 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-10809

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