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- PDB-9wym: CryoEM structure of native quinol dependent Nitric Oxide Reductas... -

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Basic information

Entry
Database: PDB / ID: 9wym
TitleCryoEM structure of native quinol dependent Nitric Oxide Reductase with HQN at pH 6.5
ComponentsNitric oxide reductase subunit B
KeywordsMEMBRANE PROTEIN / quinol-dependent Nitric Oxide Reductase
Function / homology
Function and homology information


nitric oxide reductase (cytochrome c) / nitric oxide reductase activity
Similarity search - Function
: / Nitric oxide reductase subunit B, cytochrome c-like domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / benzene-1,2,4-triol / Chem-UQ5 / Nitric oxide reductase subunit B
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKhaja, F. / Antonyuk, S.V. / Muench, S.P. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X015491/1 United Kingdom
CitationJournal: ACS Bio Med Chem Au / Year: 2026
Title: CryoEM Structures of Native Quinol-Dependent Nitric Oxide Reductase in Resting and Quinol-Bound States.
Authors: Faisal T Khaja / Allegra Mboukou / Louie P Aspinall / Charlotte E Hawksworth / Robert R Eady / Svetlana V Antonyuk / Stephen P Muench / S Samar Hasnain /
Abstract: The membrane-bound quinol-dependent nitric oxide reductases (qNORs), which are members of the respiratory heme-copper oxidase superfamily, are of major importance to food production, environment, and ...The membrane-bound quinol-dependent nitric oxide reductases (qNORs), which are members of the respiratory heme-copper oxidase superfamily, are of major importance to food production, environment, and human health. They are unique to bacteria and catalyze N-N bond formation, converting nitric oxide (NO) to generate the enzymatic product, nitrous oxide (NO), in agricultural and pathogenic conditions. High-resolution qNOR structures have been reported from two bacterial species, in which the molecular size of the protein was increased by the insertion of apocytochrome b (BRIL) at the C-terminus to facilitate cryoEM structure determination. However, it remains uncertain how BRIL fusion alters the native structure of these metalloenzymes. Here, we present the first high-resolution structure of qNOR (qNOR) determined without a fusion tag at two different pH values, revealing structural differences near the catalytic core as well as overall conformational changes between the native and fusion-tagged structures. The native enzyme shows a bell-shaped pH dependence of enzymatic activity, like nitrite reductase, the preceding enzyme in the denitrification pathway, which generates the substrate NO. In addition, we report structures of qNOR bound to quinol and hydroxyquinol that provide valuable insight into the potential electron transfer pathway originating from Trp718 to the redox centers.
History
DepositionSep 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide reductase subunit B
B: Nitric oxide reductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,66718
Polymers169,4502
Non-polymers5,21716
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Nitric oxide reductase subunit B / Nitric-oxide reductase large subunit


Mass: 84724.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter xylosoxidans (bacteria) / Gene: norB_1, ERS451415_02175, IUJ48_17015 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0ABF7PH53, nitric oxide reductase (cytochrome c)
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 6 types, 519 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#6: Chemical
ChemComp-HQN / benzene-1,2,4-triol


Mass: 126.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: quinol-dependent Nitric Oxide Reductase with Benzene-1,2,4-triol also known as hydroxyquinol (HQN)
Type: COMPLEX
Details: Two HEM and one Fe are the cofactors covalently bound to this protein. Fe is linked with one of the HEM by a water molecule via mu oxo bridge. HQN is the ligand
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Achromobacter xylosoxidans (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 767273 / Symmetry type: POINT
RefinementResolution: 2.3→2.3 Å / Cor.coef. Fo:Fc: 0.831 / SU B: 4.51 / SU ML: 0.099 / ESU R: 0.218
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.34123 --
obs0.34123 212697 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 96.109 Å2
Refinement stepCycle: 1 / Total: 11734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0150.01212139
ELECTRON MICROSCOPYr_bond_other_d00.01611305
ELECTRON MICROSCOPYr_angle_refined_deg1.4011.8216578
ELECTRON MICROSCOPYr_angle_other_deg0.451.72325797
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.25951431
ELECTRON MICROSCOPYr_dihedral_angle_2_deg11.301582
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.43101720
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0610.21750
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0214428
ELECTRON MICROSCOPYr_gen_planes_other0.0050.023112
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.459.0875737
ELECTRON MICROSCOPYr_mcbond_other8.459.0875736
ELECTRON MICROSCOPYr_mcangle_it12.5916.357161
ELECTRON MICROSCOPYr_mcangle_other12.58916.3537162
ELECTRON MICROSCOPYr_scbond_it9.44510.0736402
ELECTRON MICROSCOPYr_scbond_other9.40710.0766399
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other14.41218.0969417
ELECTRON MICROSCOPYr_long_range_B_refined24.799107.0850583
ELECTRON MICROSCOPYr_long_range_B_other24.8107.0850579
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.178 15775 -
obs--100 %

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