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- EMDB-71416: Yeast Respiratory SuperComplex - non uniform refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-71416
TitleYeast Respiratory SuperComplex - non uniform refinement
Map dataYeast Respiratory SuperComplex
Sample
  • Complex: CIII2-CIV2 Yeast respiratory supercomplex
KeywordsYeast Respiratory SuperComplex / ELECTRON TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBaker ML
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1942763 United States
Department of Energy (DOE, United States)DE-SC0022956 United States
Department of Energy (DOE, United States)DE-SC0010575 United States
CitationJournal: Nat Commun / Year: 2026
Title: Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes.
Authors: Chun Kit Chan / Jonathan Nguyen / Corey F Hryc / Chitrak Gupta / Kevin Redding / William Dowhan / Matthew L Baker / Alberto Perez / Eugenia Mileykovskaya / Abhishek Singharoy /
Abstract: The exact biological role of mitochondrial supercomplexes remains debated, particularly their role in guiding redox proteins across membranes during energy conversion. We integrate multiscale ...The exact biological role of mitochondrial supercomplexes remains debated, particularly their role in guiding redox proteins across membranes during energy conversion. We integrate multiscale modeling and single particle cryo-electron microscopy (cryo-EM) to examine electron transfer in mitochondrial supercomplexes composed of complexes III and IV (CIII and CIV). Using bioinformatic and entropy-based methods, we generated structural ensembles capturing conformations of CIII's disordered QCR6 hinge within the yeast CIII2CIV2 supercomplex. Molecular and Brownian Dynamics simulations reveal that these negatively charged hinge states electrostatically couple with redox proteins, promoting their binding and directional diffusion across the membrane on millisecond timescales. Rather than hindering transfer, disorder lowers the diffusion barrier. Anionic lipids reinforce this recognition by retaining a membrane pool of redox proteins when hinge length is critical. Cryo-EM models of ΔQCR6 show large rearrangements, yet maintain a robust electrostatic environment enabling surface-mediated transfer despite reduced charge. Overall, electron carriers confined on bioenergetic membranes follow a refolding-guided diffusion mechanism that enhances supercomplex energy conversion efficiency by nearly 30%.
History
DepositionJun 24, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71416.png

Downloads & links

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Map

FileDownload / File: emd_71416.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast Respiratory SuperComplex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.285
Minimum - Maximum-0.43572193 - 1.463976
Average (Standard dev.)0.005472815 (±0.05229246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Yeast Respiratory SuperComplex - half map

Fileemd_71416_half_map_1.map
AnnotationYeast Respiratory SuperComplex - half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Yeast Respiratory SuperComplex - half map

Fileemd_71416_half_map_2.map
AnnotationYeast Respiratory SuperComplex - half 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 : CIII2-CIV2 Yeast respiratory supercomplex

EntireName: CIII2-CIV2 Yeast respiratory supercomplex
Components
  • Complex: CIII2-CIV2 Yeast respiratory supercomplex

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Supramolecule #1: CIII2-CIV2 Yeast respiratory supercomplex

SupramoleculeName: CIII2-CIV2 Yeast respiratory supercomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66008
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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