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- EMDB-55837: Structure of human mitochondrial COX1-translating ribosome nascen... -

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Basic information

Entry
Database: EMDB / ID: EMD-55837
TitleStructure of human mitochondrial COX1-translating ribosome nascent chain complex with tRNAs in classical pre-translocation state (AP)
Map data
Sample
  • Complex: Human mitochondrial 55S ribosome complex with tRNAs and COX1 nascent chain
Keywordsmt55S / ribosome / micochondria / COX1 / membrane / translation
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSchoendorf T / Petrychenko V / Kotan I / Cruz-Zaragoza LD / Dahal D / Wang C / Gal T / Dennerlein S / Kramer G / Fischer N / Rehling P
Funding supportEuropean Union, Germany, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)ERCAdG No. 101095062European Union
German Research Foundation (DFG)SFB1565 Germany
Max Planck Society Germany
Germanys Excellence Strategy390729940 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed.
Authors: Thomas Schöndorf / Valentyn Petrychenko / Ilgin Kotan / Drishan Dahal / Natalia Napieraj / Luis Daniel Cruz-Zaragoza / Cong Wang / Oliver Urbach / Tanja Gall / Sven Dennerlein / Günter ...Authors: Thomas Schöndorf / Valentyn Petrychenko / Ilgin Kotan / Drishan Dahal / Natalia Napieraj / Luis Daniel Cruz-Zaragoza / Cong Wang / Oliver Urbach / Tanja Gall / Sven Dennerlein / Günter Kramer / Niels Fischer / Peter Rehling /
Abstract: The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ...The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not sufficiently understood. Here, we applied ribosome profiling to assess translation dynamics in combination with cryo-electron microscopy analysis of a COX1 ribosome-nascent chain complex to visualize cotranslational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation pausing events. Thus, our findings reveal a link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane.
History
DepositionNov 26, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55837.png

Downloads & links

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Map

FileDownload / File: emd_55837.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 400 pix.
= 464. Å		1.16 Å/pix.
x 400 pix.
= 464. Å		1.16 Å/pix.
x 400 pix.
= 464. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.7511649 - 2.9951842
Average (Standard dev.)0.0024861165 (±0.15897399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 464.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55837_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_55837_half_map_1.map
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Half map: #2

Fileemd_55837_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human mitochondrial 55S ribosome complex with tRNAs and COX1 nasc...

EntireName: Human mitochondrial 55S ribosome complex with tRNAs and COX1 nascent chain
Components
  • Complex: Human mitochondrial 55S ribosome complex with tRNAs and COX1 nascent chain

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Supramolecule #1: Human mitochondrial 55S ribosome complex with tRNAs and COX1 nasc...

SupramoleculeName: Human mitochondrial 55S ribosome complex with tRNAs and COX1 nascent chain
type: complex / ID: 1 / Parent: 0
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 / Details: Methods part of the manuscript
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 54447 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2068820
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

13981

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72838
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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