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- EMDB-70533: Human 28S in complex with mtIF2 and mtIF3 -

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Basic information

Entry
Database: EMDB / ID: EMD-70533
TitleHuman 28S in complex with mtIF2 and mtIF3
Map data28S-mtIF2-mtIF3
Sample
  • Complex: human mitochondrial 28S complex with mtIF2 and mtIF3
Keywordsmitochondrial ribosome mtIF2 mtIF3 / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsKober DL / Wang J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM141261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM155152 United States
Welch FoundationI-2218-20240404 United States
CitationJournal: Nat Commun / Year: 2026
Title: Mechanisms of human mitochondrial leaderless mRNA translation initiation.
Authors: Shuangjie Shen / Yinghua Xu / Daniel L Kober / Jinfan Wang /
Abstract: Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ...Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ribosomes initiate translation remain poorly understood, particularly because mitochondrial mRNAs generally lack the 5' untranslated regions that guide translation initiation in bacterial and cytoplasmic systems. Using real-time single-molecule fluorescence measurements, biochemical assays, and cryo-EM analysis, we show that human mitochondrial translation initiation occurs through two parallel pathways. In one pathway, leaderless mRNA first loads onto the 28S small subunit, followed by recruitment of the 39S large subunit to form the 55S initiation complex. In the second pathway, a preassembled 55S monosome directly loads onto leaderless mRNA. Both pathways require recruitment of mtIF2 and fMet-tRNA before mRNA binding. However, the monosome-loading pathway tolerates non-formylated Met-tRNA and is suppressed by mtIF3. Together, these findings define the heterogeneous pathways of human mitochondrial translation initiation on leaderless mRNAs.
History
DepositionMay 7, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70533.png

Downloads & links

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Map

FileDownload / File: emd_70533.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation28S-mtIF2-mtIF3
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 495.6 Å		0.83 Å/pix.
x 600 pix.
= 495.6 Å		0.83 Å/pix.
x 600 pix.
= 495.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.32129943 - 0.72972256
Average (Standard dev.)-0.00022021245 (±0.020313567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 495.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_70533_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70533_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human mitochondrial 28S complex with mtIF2 and mtIF3

EntireName: human mitochondrial 28S complex with mtIF2 and mtIF3
Components
  • Complex: human mitochondrial 28S complex with mtIF2 and mtIF3

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Supramolecule #1: human mitochondrial 28S complex with mtIF2 and mtIF3

SupramoleculeName: human mitochondrial 28S complex with mtIF2 and mtIF3 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Location in cell: mitochondria

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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