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- PDB-8zgo: CryoEM structure of monomeric quinol dependent nitric oxide reduc... -

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Basic information

Entry
Database: PDB / ID: 8zgo
TitleCryoEM structure of monomeric quinol dependent nitric oxide reductase from Neisseria meningitidis
ComponentsNitric-oxide reductase
KeywordsOXIDOREDUCTASE / Monomer / Heme / Redox / Nitric Oxide
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
: / PROTOPORPHYRIN IX CONTAINING FE / Nitric-oxide reductase
Similarity search - Component
Biological speciesNeisseria meningitidis alpha14 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsGopalasingam, C.C. / Shiro, Y. / Tosha, T.
Funding support Japan, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitric-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7185
Polymers84,3891
Non-polymers1,3294
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nitric-oxide reductase


Mass: 84389.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis alpha14 (bacteria)
Gene: norB, NMO_1451 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: C6S880, nitric-oxide reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: Monomeric quinol dependent nitric oxide reductase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.085 MDa / Experimental value: NO
Source (natural)Organism: Neisseria meningitidis alpha14 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41 (DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
10.15 MSodium ChlorideNaCl1
20.05 M2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
30.1 %decyl-thio-maltosideDTM1
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: Blot foce 3, blot time 3s

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (min): 77 K
Image recordingAverage exposure time: 3.66 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8100
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.1.1CTF correction
7UCSF ChimeraX1.4model fitting
9cryoSPARC4.1.1initial Euler assignment
10cryoSPARC4.1.1final Euler assignment
11cryoSPARC4.1.1classification
12cryoSPARC4.1.13D reconstruction
13PHENIX1.2model refinement
CTF correctionDetails: Patch based CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4640985
Details: cryoSPARC blob based picking to generate 2D templates for template based picking.
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274346 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036144
ELECTRON MICROSCOPYf_angle_d0.5918405
ELECTRON MICROSCOPYf_dihedral_angle_d7.036809
ELECTRON MICROSCOPYf_chiral_restr0.039905
ELECTRON MICROSCOPYf_plane_restr0.0041031

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