[English] 日本語
Yorodumi
- EMDB-44775: Tethered respiratory III2IV2 supercomplex from Saccharomyces cere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44775
TitleTethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae, CIVb local refinement
Map dataTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement
Sample
  • Complex: Tethered supercomplex
    • Complex: Ubiquinol-cytochrome c oxidoreductase
    • Complex: Cytochrome c oxidase
KeywordsComplex / Oxidoreductase / Respiration / ELECTRON TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsEldeeb MH / Carlstrom A / Berndtsson J / Ott M / Fontanesi F
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W911NF-21-1-0359 United States
CitationJournal: Nat Commun / Year: 2026
Title: Mitochondrial respirasome-like supercomplexes support metabolic flexibility in yeast.
Authors: Mazzen H Eldeeb / Zoe Cosner / Andreas Carlström / Jeffri-Noelle Mays / Gabriella F Rodriguez / Jens Berndtsson / Martin Ott / Flavia Fontanesi /
Abstract: The mitochondrial respiratory chain (MRC) complexes, crucial for aerobic energy transduction in eukaryotes, form conserved higher-order structures called supercomplexes (SCs). The elucidation of SC ...The mitochondrial respiratory chain (MRC) complexes, crucial for aerobic energy transduction in eukaryotes, form conserved higher-order structures called supercomplexes (SCs). The elucidation of SC physiological relevance is critical for our understanding of mitochondrial function and bioenergetics but has been hindered by the limited availability of experimental models isolating SC formation as the sole variable. In baker's yeast, SCs comprise IIIIV and IIIIV configurations, which enhance respiratory rates by facilitating cytochrome c diffusion along the SC surface. However, the roles of distinct SC conformations and MRC plasticity remain unclear. To address these questions, we engineered a yeast strain expressing a covalently-linked IIIIV SC, structurally like the wild-type. Expression of this tethered SC supports robust respiratory activity but selectively impacts cytosolic NADH-driven respiration, due to distinct interactions with the NADH dehydrogenase Nde1. We propose that in yeast mitochondria, substrate-specific respirasome-like SCs contribute to the optimization of electron fluxes and support metabolic flexibility.
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44775.png

Downloads & links

-
Map

FileDownload / File: emd_44775.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 450 pix.
= 508.05 Å		1.13 Å/pix.
x 450 pix.
= 508.05 Å		1.13 Å/pix.
x 450 pix.
= 508.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.129 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.8561381 - 2.8251507
Average (Standard dev.)-0.0012949379 (±0.07304206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 508.05 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_44775_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Tethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local...

Fileemd_44775_half_map_1.map
AnnotationTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Tethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local...

Fileemd_44775_half_map_2.map
AnnotationTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tethered supercomplex

EntireName: Tethered supercomplex
Components
  • Complex: Tethered supercomplex
    • Complex: Ubiquinol-cytochrome c oxidoreductase
    • Complex: Cytochrome c oxidase

-
Supramolecule #1: Tethered supercomplex

SupramoleculeName: Tethered supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

-
Supramolecule #2: Ubiquinol-cytochrome c oxidoreductase

SupramoleculeName: Ubiquinol-cytochrome c oxidoreductase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

-
Supramolecule #3: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#21
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris-HCl pH 7.5
150.0 mMNaClSodium chloride
1.0 mMC7H7FO2SPhenylmethylsulfonyl fluoride (PMSF)
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid (EDTA)
0.1 %C56H92O29Digitonin
150.0 ng/uLC120H169N31O49S3X FLAG peptide
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: The grid was covered in a 3 nm ultrathin carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: 3 uL of sample, 5 s blot time, 30 s hold time, 0 blot force..

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12211 / Average exposure time: 2.6 sec. / Average electron dose: 55.452 e/Å2
Details: Images were collected as movies composed of 40 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1646359
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial model for refinement was generated ab-initio in cryoSPARC.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 47746
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2) / Details: Local refinement after particle subtraction
Final 3D classificationNumber classes: 5 / Avg.num./class: 9785 / Software - Name: cryoSPARC (ver. 4.2)
Details: Classification was performed in 3D to remove junk particles from the dataset. The final round of classification used 48,925 particles, with 48,218 ultimately being used for refinement of the predominant class.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6ymx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL

+
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