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- PDB-8zgp: CryoEM structure of dimeric quinol dependent nitric oxide reducta... -

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Basic information

Entry
Database: PDB / ID: 8zgp
TitleCryoEM structure of dimeric quinol dependent nitric oxide reductase from Neisseria meningitidis
ComponentsNitric-oxide reductase
KeywordsOXIDOREDUCTASE / Heme / Redox / Nitric Oxide / Dimer
Function / homology
Function and homology information


nitric-oxide reductase / cytochrome-c oxidase activity / aerobic respiration / heme binding / metal ion binding / membrane
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: 1.89 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: To Be Published
Title: CryoEM structure of dimeric quinol dependent nitric oxide reductase from Neisseria meningitidis
Authors: Gopalasingam, C.C. / Shiro, Y. / Tosha, T.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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
B: Nitric-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,43610
Polymers168,7782
Non-polymers2,6588
Water2,270126
1


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

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Components

#1: Protein Nitric-oxide reductase


Mass: 84389.211 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: Dimeric quinol dependent nitric oxide reductase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.17 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
30.05 %decyl-thio-maltosideDTM1
SpecimenConc.: 35 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: 277 K

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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: 2.26 sec. / Electron dose: 51.19 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7525
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
7UCSF ChimeraX1.4model fitting
9PHENIX1.15model refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2574970
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 357535 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6l3h

6l3h


Accession code: 6l3h / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412436
ELECTRON MICROSCOPYf_angle_d0.66617014
ELECTRON MICROSCOPYf_dihedral_angle_d7.6561636
ELECTRON MICROSCOPYf_chiral_restr0.0441812
ELECTRON MICROSCOPYf_plane_restr0.0052094

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