› 3jq4

X-ray diffraction
3.52Å resolution

The structure of the complex of the large ribosomal subunit from D. Radiodurans with the antibiotic lankacidin

Released:
DOI: 10.2210/pdb3jq4/pdb
PDB entry 3jq4 coloured by chain, front view.
PDB entry 3jq4 coloured by chain, side view.
PDB entry 3jq4 coloured by chain, top view.
Source organism: Deinococcus radiodurans R1
Primary publication:
The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics.
Auerbach T, Mermershtain I, Davidovich C, Bashan A, Belousoff M, Wekselman I, Zimmerman E, Xiong L, Klepacki D, Arakawa K, Kinashi H, Mankin AS, Yonath A
Proc Natl Acad Sci U S A 107 1983-8 (2010)
PMID: 20080686

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-195821 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Source organism: Deinococcus radiodurans R1
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 118 nucleotides
Theoretical weight: 38.03 KDa
Source organism: Deinococcus radiodurans R1
Sequence domains: 5S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand LC2 1 x LC2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID, ESRF BEAMLINE ID23-2
Spacegroup: I222
Unit cell:
a: 169.8Å b: 410.3Å c: 694.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.268 0.268 0.325

Quick links

Citations

11 review citations

Ribosome-targeting antibiotics and mechanisms of bacterial resistance.
Wilson DN. (2014)
10 more

3 mentions without citation

Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
Belousoff et al. (2011)
2 more