[English] 日本語
Yorodumi
- EMDB-83586: Cryo-EM structure of monomeric bovine heart cytochrome c oxidase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-83586
TitleCryo-EM structure of monomeric bovine heart cytochrome c oxidase in amphipol A8-35
Map data
Sample
  • Complex: Cytochrome c oxidase
KeywordsCytochrome c oxidase / Amphipol A8-35 / Monomer / Cryo-EM / OXIDOREDUCTASE
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsChesnokov YM / Nesterov SV
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian FederationAAAA-A19-119031390114-5 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2026
Title: Reversible Dimerization of Cytochrome Oxidase in Detergent Solution as Detected by Dynamic Light Scattering
Authors: Azarkina NV / Orlov NV / Muntyan MS / Chesnokov YM / Nesterov SV / Oleynikov IP / Vygodina TV
History
DepositionSep 12, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_83586.png

Downloads & links

-
Map

FileDownload / File: emd_83586.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 223.744 Å		0.87 Å/pix.
x 256 pix.
= 223.744 Å		0.87 Å/pix.
x 256 pix.
= 223.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.874 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.3228782 - 0.6433598
Average (Standard dev.)0.0031288452 (±0.029336631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 223.744 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_83586_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_83586_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_83586_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cytochrome c oxidase

EntireName: Cytochrome c oxidase
Components
  • Complex: Cytochrome c oxidase

-
Supramolecule #1: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / ID: 1 / Parent: 0
Details: Monomeric bovine heart cytochrome c oxidase (complex IV, 13 subunits) solubilized in amphipol A8-35 (AmM preparation).
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Heart / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane
Molecular weightTheoretical: 204.5 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Component - Concentration: 50.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES / Details: 50 mM HEPES/NaOH, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
Details: Glow-discharged for 20 s at 20 mA using a PELCO easiGlow system.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMonomeric bovine cytochrome c oxidase in complex with amphipol A8-35, purified from bovine heart mitochondria.

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 80.0 K
Specialist opticsSpherical aberration corrector: Cs image corrector (CEOS GmbH)
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsCs corrected, 3x3 holes (2 exposures per hole) image-shift data acquisition strategy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 1011 / Average exposure time: 3.5 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 57208 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 20739
CTF correctionSoftware:
Namedetails
Warp (ver. 1.9)CTF estimation
cryoSPARC (ver. 4.6)CTF refinement

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio reconstruction in cryoSPARC
Details: Ab initio reconstruction with two classes at a maximum resolution of 6 A using 20,739 particles
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 7428
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.6) / Software - details: Ab initio reconstruction
Details: Stochastic gradient descent during ab initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6) / Software - details: Non-uniform refinement
Details: Non-uniform refinement, CTF refinement, second round of non-uniform refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 10370 / Software - Name: cryoSPARC (ver. 4.6) / Software - details: Ab initio reconstruction (2 classes)
Details: Multi-class ab initio reconstruction; the major class (7,428 particles) consistent with the monomeric CcO structure was selected, the remaining particles were discarded.
FSC plot (resolution estimation)

+
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