› 6rko

Electron Microscopy
2.68Å resolution

Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution

Released:
DOI: 10.2210/pdb6rko/pdb
PDB entry 6rko coloured by chain, front view.
PDB entry 6rko coloured by chain, side view.
PDB entry 6rko coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.
Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kühlbrandt W, Michel H
Science 366 100-104 (2019)
PMID: 31604309
Related structures: EMD-4908

Function and Biology Details

Reaction catalysed: 
(1a) 2 ubiquinol = 2 ubiquinone + 4 H(+)(Side 1) + 4 e(-)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-107541 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Cytochrome bd-I ubiquinol oxidase subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 379 amino acids
Theoretical weight: 42.48 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ABK2 (Residues: 1-379; Coverage: 100%)
Gene names: JW0723, b0734, cyd-2, cydB
Sequence domains: Cytochrome bd terminal oxidase subunit II
Cytochrome bd-I ubiquinol oxidase subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 522 amino acids
Theoretical weight: 58.25 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ABJ9 (Residues: 1-522; Coverage: 100%)
Gene names: JW0722, b0733, cyd-1, cydA
Sequence domains: Cytochrome bd terminal oxidase subunit I
Uncharacterized protein YnhF Chain: H
Molecule details ›
Chain: H
Length: 29 amino acids
Theoretical weight: 3 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: A5A618 (Residues: 1-29; Coverage: 100%)
Gene names: JW1649.1, b4602, ynhF
Cytochrome bd-I ubiquinol oxidase subunit X Chain: X
Molecule details ›
Chain: X
Length: 37 amino acids
Theoretical weight: 4.04 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P56100 (Residues: 1-37; Coverage: 100%)
Gene names: JW0724, b4515, cydX, ybgT
Sequence domains: Membrane bound YbgT-like protein

Ligands and Environments

5 bound ligands:
Ligand UQ8 1 x UQ8
Ligand POV 4 x POV
Ligand HDD 1 x HDD
Ligand HEB 2 x HEB
Ligand OXY 1 x OXY
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.68Å
Relevant EMDB volumes: EMD-4908
Expression system: Escherichia coli

Quick links

Citations

9 review citations

ROS Defense Systems and Terminal Oxidases in Bacteria.
Borisov et al. (2021)
8 more

12 mentions without citation

Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets.
Borisov et al. (2021)
11 more