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› 7nri

Electron Microscopy
3.03Å resolution

Structure of the darobactin-bound E. coli BAM complex (BamABCDE)

Released:
DOI: 10.2210/pdb7nri/pdb
PDB entry 7nri coloured by chain, front view.
PDB entry 7nri coloured by chain, side view.
PDB entry 7nri coloured by chain, top view.
Source organisms:
Primary publication:
The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase.
Kaur H, Jakob RP, Marzinek JK, Green R, Imai Y, Bolla JR, Agustoni E, Robinson CV, Bond PJ, Lewis K, Maier T, Hiller S
Nature 593 125-129 (2021)
PMID: 33854236
Related structures: EMD-12546

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-141768 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Outer membrane protein assembly factor BamA Chain: A
Molecule details ›
Chain: A
Length: 788 amino acids
Theoretical weight: 88.23 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A940 (Residues: 21-808; Coverage: 100%)
Gene names: JW0172, b0177, bamA, yaeT, yzzN, yzzY
Sequence domains:
Outer membrane protein assembly factor BamB Chain: B
Molecule details ›
Chain: B
Length: 381 amino acids
Theoretical weight: 40.92 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P77774 (Residues: 20-392; Coverage: 100%)
Gene names: JW2496, b2512, bamB, yfgL
Sequence domains:
Outer membrane protein assembly factor BamC Chain: C
Molecule details ›
Chain: C
Length: 320 amino acids
Theoretical weight: 34.4 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A903 (Residues: 25-344; Coverage: 100%)
Gene names: JW2462, b2477, bamC, dapX, nlpB
Sequence domains: NlpB/DapX lipoprotein
Outer membrane protein assembly factor BamD Chain: D
Molecule details ›
Chain: D
Length: 226 amino acids
Theoretical weight: 25.82 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AC02 (Residues: 20-245; Coverage: 100%)
Gene names: JW2577, b2595, bamD, yfiO
Sequence domains: Outer membrane lipoprotein
Outer membrane protein assembly factor BamE Chain: E
Molecule details ›
Chain: E
Length: 102 amino acids
Theoretical weight: 11.46 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A937 (Residues: 20-113; Coverage: 100%)
Gene names: JW2598, b2617, bamE, smpA
Sequence domains: Outer membrane protein assembly factor BamE domain
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE Chain: G
Molecule details ›
Chain: G
Length: 7 amino acids
Theoretical weight: 971 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand UX8 1 x UX8

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.03Å
Relevant EMDB volumes: EMD-12546
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

26 review citations

Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides.
Ongpipattanakul et al. (2022)
25 more

6 mentions without citation

ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics.
George et al. (2024)
5 more