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- EMDB-66368: CryoEM structure of quinol dependent Nitric Oxide Reductase with BRIL -

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Basic information

Entry
Database: EMDB / ID: EMD-66368
TitleCryoEM structure of quinol dependent Nitric Oxide Reductase with BRIL
Map data
Sample
  • Complex: quinol-dependent Nitric Oxide Reductase with BRIL
    • Protein or peptide: Nitric oxide reductase subunit B,Soluble cytochrome b562
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FE (III) ION
  • Ligand: CALCIUM ION
Keywordsquinol-dependent Nitric Oxide Reductase / MEMBRANE PROTEIN
Function / homology
Function and homology information


nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Nitric oxide reductase subunit B / Soluble cytochrome b562
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKhaja F / Mboukou A / Antonyuk SV / Muench SP / Hasnain SS
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66368.png

Downloads & links

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Map

FileDownload / File: emd_66368.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 420 pix.
= 449.4 Å		1.07 Å/pix.
x 420 pix.
= 449.4 Å		1.07 Å/pix.
x 420 pix.
= 449.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275
Minimum - Maximum-0.45043278 - 2.2366295
Average (Standard dev.)0.00085497333 (±0.04066383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 449.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66368_msk_1.map
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Additional map: sharpened map

Fileemd_66368_additional_1.map
Annotationsharpened map
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Half map: #2

Fileemd_66368_half_map_1.map
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Half map: #1

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Sample components

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Entire : quinol-dependent Nitric Oxide Reductase with BRIL

EntireName: quinol-dependent Nitric Oxide Reductase with BRIL
Components
  • Complex: quinol-dependent Nitric Oxide Reductase with BRIL
    • Protein or peptide: Nitric oxide reductase subunit B,Soluble cytochrome b562
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FE (III) ION
  • Ligand: CALCIUM ION

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Supramolecule #1: quinol-dependent Nitric Oxide Reductase with BRIL

SupramoleculeName: quinol-dependent Nitric Oxide Reductase with BRIL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: BRIL-AxqNOR. Two HEM and one Fe are the cofactors covalently bound to this protein.
Source (natural)Organism: Achromobacter xylosoxidans (bacteria)

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Macromolecule #1: Nitric oxide reductase subunit B,Soluble cytochrome b562

MacromoleculeName: Nitric oxide reductase subunit B,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitric oxide reductase (cytochrome c)
Source (natural)Organism: Achromobacter xylosoxidans (bacteria)
Molecular weightTheoretical: 94.903242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGPYRRLWFT LIAVLAVTFA LLGFYGGEVY RQAPPIPEEV ASADGTRLFG RDDILDGQTA WQSIGGMQLG SIWGHGAYQA PDWTADWLH RELMAWLDLA ARDAHGRDYG QLDAPAQAAL REQLKAEYRA NRADAAGGKL TLSPRRAQAV AQTEAYYDQL F SDAPALHR ...String:
MGPYRRLWFT LIAVLAVTFA LLGFYGGEVY RQAPPIPEEV ASADGTRLFG RDDILDGQTA WQSIGGMQLG SIWGHGAYQA PDWTADWLH RELMAWLDLA ARDAHGRDYG QLDAPAQAAL REQLKAEYRA NRADAAGGKL TLSPRRAQAV AQTEAYYDQL F SDAPALHR SRENYAMKEN TLPDANRRRQ MTHFFFWTAW AAATEREGTS VTYTNNWPHE PLIGNHPSSE NVMWSIISVV VL LAGIGLL IWAWAFLRGK EEDEPPAPAR DPLTTFALTP SQRALGKYLF LVVALFGFQV LLGGFTAHYT VEGQKFYGID LSQ WFPYSL VRTWHIQSAL FWIATGFLAA GLFLAPLING GRDPKYQKAG VDILFWALVL VVVGSFAGNY LAIAQIMPPD LNFW LGHQG YEYVDLGRLW QIGKFAGICF WLVLMLRGIV PALRTPGGDK NLLALLTASV GAIGLFYGAG FFYGERTHLT VMEYW RWWI VHLWVEGFFE VFATTALAFI FSTLGLVSRR MATTASLASA SLFMLGGIPG TFHHLYFAGT TTPVMAVGAS FSALEV VPL IVLGHEAWEN WRLKTRAPWM ENLKWPLMCF VAVAFWNMLG AGVFGFMINP PVSLYYIQGL NTTPVHAHAA LFGVYGF LA LGFTLLVLRY IRPQYALSPG LMKLAFWGLN LGLALMIFTS LLPIGLIQFH ASVSEGMWYA RSEAFMQQDI LKTLRWGR T FGDVVFLLGA LAMVVQVILG LLSGKADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YL

UniProtKB: Nitric oxide reductase subunit B, Soluble cytochrome b562

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6qq5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 100494
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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