[English] 日本語
Yorodumi
- EMDB-60085: CryoEM structure of monomeric quinol dependent nitric oxide reduc... -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 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: To Be Published
Title: CryoEM structure of monomeric 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

-
Structure visualization

Supplemental images

emd_60085.png

Downloads & links

-
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
Brightness
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Additional map: #1

Fileemd_60085_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60085_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60085_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
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

+
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more