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

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Open data


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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: Shen S / Xu Y / Kober DL / Wang J
History
DepositionMay 7, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 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
Contrast
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

Projections

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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