7NKZ | pdb_00007nkz

Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB.

Safarian, S.Opel-Reading, H.K.Wu, D.Mehdipour, A.R.Hards, K.Harold, L.K.Radloff, M.Stewart, I.Welsch, S.Hummer, G.Cook, G.M.Krause, K.L.Michel, H.

(2021) Nat Commun 12: 5236-5236

  • DOI: https://doi.org/10.1038/s41467-021-25537-z
  • Primary Citation Related Structures: 
    7NKZ

  • PubMed Abstract: 

    New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective treatment options to shorten drug administration regimes, and reduce the opportunity for the emergence of drug resistance. During infection and proliferation, the cytochrome bd oxidase plays a crucial role for mycobacterial pathophysiology by maintaining aerobic respiration at limited oxygen concentrations. Here, we present the cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 Å. In conjunction with atomistic molecular dynamics (MD) simulation studies we discovered a previously unknown MK-9-binding site, as well as a unique disulfide bond within the Q-loop domain that defines an inactive conformation of the canonical quinol oxidation site in Actinobacteria. Our detailed insights into the long-sought atomic framework of the cytochrome bd oxidase from M. tuberculosis will form the basis for the design of highly specific drugs to act on this enzyme.


  • Organizational Affiliation
    • Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany. schara.safarian@biophys.mpg.de.

Macromolecule Content 

  • Total Structure Weight: 94.2 kDa 
  • Atom Count: 6,424 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 831 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)A [auth B]346Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cydBRv1622c
Membrane Entity: Yes 
UniProt
Find proteins for O06139 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06139 
Go to UniProtKB:  O06139
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06139
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)B [auth A]485Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cydARv1623c
Membrane Entity: Yes 
UniProt
Find proteins for L7N662 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore L7N662 
Go to UniProtKB:  L7N662
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7N662
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Max Planck SocietyGermanyNobel Laureate Fellowship
Marsden FundNew Zealand--
Royal Society of New ZealandNew ZealandCatalyst grant

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary