› 6pc7

Electron Microscopy
2.5Å resolution

E. coli 50S ribosome bound to compound 46

Released:
DOI: 10.2210/pdb6pc7/pdb
PDB entry 6pc7 coloured by chain, front view.
PDB entry 6pc7 coloured by chain, side view.
PDB entry 6pc7 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Synthetic group A streptogramin antibiotics that overcome Vat resistance.
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Mühle E, Chesneau O, Fraser JS, Seiple IB
Nature 586 145-150 (2020)
PMID: 32968273
Related structures: EMD-20298

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-135833 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (7 distinct):
Large ribosomal subunit protein uL2 Chain: K
Molecule details ›
Chain: K
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 2-272; Coverage: 99%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL15 Chain: L
Molecule details ›
Chain: L
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL4 Chain: M
Molecule details ›
Chain: M
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL3 Chain: N
Molecule details ›
Chain: N
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL13 Chain: O
Molecule details ›
Chain: O
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
23S ribosomal RNA Chain: I
Molecule details ›
Chain: I
Length: 2904 nucleotides
Theoretical weight: 941.8 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: J
Molecule details ›
Chain: J
Length: 118 nucleotides
Theoretical weight: 38.18 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand O7V 1 x O7V
12 modified residues:
Ligand 1MG 1 x 1MG
Ligand PSU 8 x PSU
Ligand 5MU 2 x 5MU
Ligand 6MZ 1 x 6MZ
Ligand 2MG 2 x 2MG
Ligand 3TD 1 x 3TD
Ligand 5MC 1 x 5MC
Ligand G7M 1 x G7M
Ligand OMG 1 x OMG
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-20298

Quick links

Citations

4 review citations

Molecular mechanisms of antibiotic resistance revisited.
Darby et al. (2023)
3 more