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- EMDB-60086: CryoEM structure of dimeric quinol dependent nitric oxide reducta... -

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Basic information

Entry
Database: EMDB / ID: EMD-60086
TitleCryoEM structure of dimeric quinol dependent nitric oxide reductase from Neisseria meningitidis
Map data
Sample
  • Complex: Dimeric 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
KeywordsHeme / Redox / Nitric Oxide / Dimer / OXIDOREDUCTASE
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
Nitric-oxide reductase
Similarity search - Component
Biological speciesNeisseria meningitidis alpha14 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.89 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: To Be Published
Title: CryoEM structure of dimeric quinol dependent nitric oxide reductase from Neisseria meningitidis
Authors: Gopalasingam CC / Shiro Y / Tosha T
History
DepositionMay 9, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60086.png

Downloads & links

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Map

FileDownload / File: emd_60086.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 368 pix.
= 276.736 Å		0.75 Å/pix.
x 368 pix.
= 276.736 Å		0.75 Å/pix.
x 368 pix.
= 276.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0121
Minimum - Maximum-0.052607365 - 0.18355402
Average (Standard dev.)0.0000052578916 (±0.0027156265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 276.736 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_60086_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60086_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60086_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric quinol dependent nitric oxide reductase

EntireName: Dimeric quinol dependent nitric oxide reductase
Components
  • Complex: Dimeric 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: Dimeric quinol dependent nitric oxide reductase

SupramoleculeName: Dimeric quinol dependent nitric oxide reductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neisseria meningitidis alpha14 (bacteria)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Nitric-oxide reductase

MacromoleculeName: Nitric-oxide reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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: 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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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 126 / 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

Concentration35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.15 MNaClSodium Chloride
0.05 MHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
0.05 %DTMdecyl-thio-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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 grids imaged: 1 / Number real images: 7525 / Average exposure time: 2.26 sec. / Average electron dose: 51.19 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: 2574970
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Reconstruction from small dataset obatined on Glacios
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 357535
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6l3h


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8zgp:
CryoEM structure of dimeric quinol dependent nitric oxide reductase from Neisseria meningitidis

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