PDB 7xmd structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

Electron Microscopy

2.99Å resolution

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4

Released: 21 Dec 2022

DOI: 10.2210/pdb7xmd/pdb

Source organism: Escherichia coli

Primary publication:
Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.

Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y

Nat Commun 13 7591 (2022)

PMID: 36481732

Related structures: EMD-33294

Function and Biology Details

Reaction catalysed:

2 ubiquinol + O(2) + n H(+)(Side 1) = 2 ubiquinone + 2 H(2)O + n H(+)(Side 2)

Biochemical function:

cytochrome bo3 ubiquinol oxidase activity

Biological process:

aerobic electron transport chain

Cellular component:

membrane

Sequence domains:

13 more domains

Structure analysis Details

Assembly composition:

hetero tetramer (preferred)

Assembly name:

Cytochrome bo3 ubiquinol oxidase complex (preferred)

PDBe Complex ID:

PDB-CPX-142171 (preferred)

Entry contents:

4 distinct polypeptide molecules

Macromolecules (4 distinct):

Cytochrome bo(3) ubiquinol oxidase subunit 1 Chain: A

Molecule details ›

Chain: A
Length: 663 amino acids
Theoretical weight: 74.42 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:

Canonical: P0ABI8 (Residues: 1-663; Coverage: 100%)

Gene names: JW0421, b0431, cyoB
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I

Cytochrome bo(3) ubiquinol oxidase subunit 2 Chain: B

Molecule details ›

Chain: B
Length: 324 amino acids
Theoretical weight: 36.21 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:

Canonical: P0ABJ1 (Residues: 1-315; Coverage: 100%)

Gene names: JW0422, b0432, cyoA
Sequence domains:

Cytochrome bo(3) ubiquinol oxidase subunit 3 Chain: C

Cytochrome bo(3) ubiquinol oxidase subunit 4 Chain: D

Ligands and Environments

6 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores

Resolution: 2.99Å

Relevant EMDB volumes: EMD-33294

Expression system: Escherichia coli

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Citations

1 citations in other articles

Antimicrobial effects of Medicines for Malaria Venture Pathogen Box compounds on strains of Neisseria gonorrhoeae.

Mensah et al. (2023)