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- EMDB-60085: CryoEM structure of monomeric quinol dependent nitric oxide reduc... -

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Basic information

Entry
Database: EMDB / ID: EMD-60085
TitleCryoEM structure of monomeric quinol dependent nitric oxide reductase from Neisseria meningitidis
Map data
Sample
  • Complex: Monomeric quinol dependent nitric oxide reductase
    • Protein or peptide: Nitric-oxide reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FE (III) ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsMonomer / Heme / Redox / Nitric Oxide / OXIDOREDUCTASE
Function / homology
Function and homology information


nitric-oxide reductase / cytochrome-c oxidase activity / aerobic respiration / oxidoreductase activity / heme binding / membrane / metal ion 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
Similarity search - Domain/homology
Nitric-oxide reductase
Similarity search - Component
Biological speciesNeisseria meningitidis alpha14 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsGopalasingam CC / Shiro Y / Tosha T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H05761 Japan
Japan Society for the Promotion of Science (JSPS)JP20K22633 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Structural basis of Neisseria meningitidis quinol dependent nitric oxide reductase activation by dimerization.
Authors: Chai C Gopalasingam / Haruka Egami / Hideki Shigematsu / Masatora Sakaue / Kouki Fukumoto / Christoph Gerle / Masaki Yamamoto / Yoshitsugu Shiro / Kazumasa Muramoto / Takehiko Tosha /
Abstract: In all kingdoms of life, the regulation of membrane-bound enzyme function via oligomerization is a fundamental aspect of cell physiology. Often, the mechanistic role of oligomerization is unclear, ...In all kingdoms of life, the regulation of membrane-bound enzyme function via oligomerization is a fundamental aspect of cell physiology. Often, the mechanistic role of oligomerization is unclear, due to a lack of structure-function comparisons between constituent forms of the enzyme. Here, we elucidate the structural underpinnings of enzyme regulation and oligomerization in the quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis, by high-resolution structural analyses of the less active monomeric form (2.25 Å) and the highly active dimeric form (1.89 Å). The comparison revealed that broad helical flexibility near the dimer interface of the monomer causes a conformational change in a critical amino acid near the active site, located apart from the dimer interface. We demonstrate that the crosstalk between the dimer interface and catalytic site in qNOR allows enhanced activation of the enzyme via dimerization. Given Neisseria meningitidis' dependence on qNOR to detoxify the host's immune response of nitric oxide, our results pave a way for new strategies to combat bacterial infections, via the inactivation of qNOR by monomerization. More broadly, this provides new insights into the role of membrane protein oligomerization and its influence on regulating activity.
History
DepositionMay 9, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60085.png

Downloads & links

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Map

FileDownload / File: emd_60085.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 324 pix.
= 270.864 Å		0.84 Å/pix.
x 324 pix.
= 270.864 Å		0.84 Å/pix.
x 324 pix.
= 270.864 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-0.3028032 - 0.91671324
Average (Standard dev.)0.00009616341 (±0.016056646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 270.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_60085_additional_1.map
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Half map: #1

Fileemd_60085_half_map_1.map
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Half map: #2

Fileemd_60085_half_map_2.map
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Sample components

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Entire : Monomeric quinol dependent nitric oxide reductase

EntireName: Monomeric quinol dependent nitric oxide reductase
Components
  • Complex: Monomeric quinol dependent nitric oxide reductase
    • Protein or peptide: Nitric-oxide reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FE (III) ION
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Monomeric quinol dependent nitric oxide reductase

SupramoleculeName: Monomeric quinol dependent nitric oxide reductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neisseria meningitidis alpha14 (bacteria)
Molecular weightTheoretical: 85 KDa

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Macromolecule #1: Nitric-oxide reductase

MacromoleculeName: Nitric-oxide reductase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: nitric-oxide reductase
Source (natural)Organism: Neisseria meningitidis alpha14 (bacteria)
Molecular weightTheoretical: 84.389211 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGQYKKLWYL LFAVLAVCFT ILGYMGSEVY KKAPPYPEQV VSASGKVLMA KDDILAGQSA WQTTGGMEVG SVLGHGAYQA PDWTADWLH RELSAWLDLT AQQTYGKKFD EVSPEEQAVL KTRLADEYRN QSRIKEDGSV VISDTRVKAI ESILPYYHGV Y GDDPALQT ...String:
MGQYKKLWYL LFAVLAVCFT ILGYMGSEVY KKAPPYPEQV VSASGKVLMA KDDILAGQSA WQTTGGMEVG SVLGHGAYQA PDWTADWLH RELSAWLDLT AQQTYGKKFD EVSPEEQAVL KTRLADEYRN QSRIKEDGSV VISDTRVKAI ESILPYYHGV Y GDDPALQT TREHFAMKNN TLPSQEAREK LFDFFFWTSW SASTNRPDET FTYTNNWPHE PLINNVPTTE NYMWSFTSVV LL LMGIGLL MWGYSFLTKH EEVEVPTEDP ISKVQLTPSQ KALGKYVFLT VALFVVQVLL GGLTAHYTVE GQGFYGIDEA LGF EMSDWF PYALTRTWHI QSAIFWIATG FLTAGLFLAP IVNGGKDPKF QRAGVNFLYI ALFIVVGGSY AGNFFALTHI LPPE FNFWF GHQGYEYLDL GRFWQLLLMV GLLLWLFLML RCTVSAFKEK GVDKNLLAIF VASMVGVGVF YAPGLFYGEK SPIAV MEYW RWWVVHLWVE GFFEVFATAA FAFVFYNMGF VRRSTATAST LAAAAIFMLG GVPGTLHHLY FSGSTSASMA IGACFS ALE VVPLVLLGRE AYEHWSYQHL SEWAKRLRWP LMCFVAVAFW NMIGAGVFGF LINPPISLFY IQGLNTSAVH AHAALFG VY GFLALGFVLL VARYLKPNVQ FDDKLMTWGF WLLNGGLVGM IAISLLPVGV IQAYASITHG LWYARSEEFL QMEILDTL R WVRTAADLIF IGGAICVAIQ ATKIVFGRDK

UniProtKB: Nitric-oxide reductase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / 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: 1 / 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: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.15 MNaClSodium Chloride
0.05 MHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
0.1 %DTMdecyl-thio-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Blot foce 3, blot time 3s.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
TemperatureMin: 77.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 8100 / Average exposure time: 3.66 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 4640985
Details: cryoSPARC blob based picking to generate 2D templates for template based picking.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.1) / Details: Patch based CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 274346
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1) / Details: Ab initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8zgo:
CryoEM structure of monomeric quinol dependent nitric oxide reductase from Neisseria meningitidis

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