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- EMDB-52613: NDUFA4 bound complex IV with weak density from HIGD2A -

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Basic information

Entry
Database: EMDB / ID: EMD-52613
TitleNDUFA4 bound complex IV with weak density from HIGD2A
Map data
Sample
  • Cell: Complex IV
KeywordsHuman mitochondria / respirasome complex / cytochrome c reductase / intermediates / assembly / HIGD2A / NDUFA4 / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNguyen MD / Rorbach J
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome.
Authors: Minh Duc Nguyen / Ana Sierra-Magro / Vivek Singh / Anas Khawaja / Alba Timón-Gómez / Antoni Barrientos / Joanna Rorbach /
Abstract: The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required ...The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required for ATP synthesis. These complexes can associate into supercomplexes (SCs), such as the CI + CIII₂ + CIV respirasome, but how SCs form, by joining preassembled complexes or by engaging partially assembled intermediates, remains unresolved. Here, we use cryo-electron microscopy to determine high-resolution structures of native human CI + CIII₂ + CIV late-assembly intermediates. Together with biochemical analyses, these structures show that respirasome biogenesis concludes with the final maturation of CIV while it is associated with fully assembled CI and CIII₂. We identify HIGD2A as a placeholder factor within isolated and supercomplexed CIV that is replaced by subunit NDUFA4 during the last step of CIV and respirasome assembly. This mechanism suggests that placeholders such as HIGD2A act as molecular timers, preventing premature incorporation of NDUFA4 or its isoforms and ensuring the orderly progression of pre-SC particles into functional respirasomes. Since defects in CIV assembly, including NDUFA4 deficiencies, cause severe encephalomyopathies and neurodegenerative disorders, understanding the molecular architecture and assembly pathways of isolated and supercomplexed CIV offers insight into the pathogenic mechanisms underlying these conditions.
History
DepositionJan 24, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52613.png

Downloads & links

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Map

FileDownload / File: emd_52613.map.gz / Format: CCP4 / Size: 824 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 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.8529391 - 1.7898177
Average (Standard dev.)-0.0042540194 (±0.04334129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52613_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52613_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex IV

EntireName: Complex IV
Components
  • Cell: Complex IV

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Supramolecule #1: Complex IV

SupramoleculeName: Complex IV / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
Component:
ConcentrationFormulaName
50.0 mMKClpotassium chloride
25.0 mMC8H18N2O4SHepes
20.0 mMMg(CH3COO)2Magnesium acetate
0.01 %C47H88O22LMNG

Details: 25 mM HEPES-KOH pH=7.5, 50 mM KCl, 20 mM Mg(OAc)2, 0.01% (v/v) LMNG, 0.001 % cardiolipin, 0.001 % GD, 0.1mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 38662 / Average exposure time: 3.5 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
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: PDB ENTRY
PDB model - PDB ID:

5z62

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56968
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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