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- EMDB-57668: Human mitochondrial small ribosomal subunit: Initiation complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-57668
TitleHuman mitochondrial small ribosomal subunit: Initiation complex with IF2 and tRNA (state I4)
Map data
Sample
  • Complex: mitoribosomal small subunit assembly intermediate
Keywordsmitochondria / small subunit / assembly / NOA1 / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSingh V / Shiriaev D / Khawaja A / Rorbach J
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW2019.0109 Sweden
Swedish Research CouncilVR2016-02179 Sweden
CitationJournal: Nat Commun / Year: 2026
Title: Pseudouridine synthase PUS1 and initiation factor mtIF2 are human mitoribosomal small subunit assembly factors.
Authors: Vivek Singh / Dmitrii Shiriaev / Lorina Bilalli / Anas Khawaja / Joanna Rorbach /
Abstract: Assembly of the mitochondrial ribosome (mitoribosome) is a crucial step in mitochondrial gene expression. This process facilitates mitochondrial translation, which produces essential subunits of the ...Assembly of the mitochondrial ribosome (mitoribosome) is a crucial step in mitochondrial gene expression. This process facilitates mitochondrial translation, which produces essential subunits of the oxidative phosphorylation machinery-the cell's primary energy-producing machinery. Disruptions in mitoribosome assembly can lead to severe human diseases. Given its fundamental importance, detailed structural analysis of mitoribosome assembly pathways is essential for advancing our understanding of mitochondrial function in both health and disease. In this study, we characterize twelve distinct assembly states of the mitoribosomal small subunit (mtSSU) isolated from human cells. Our findings reveal the intricate details of the final maturation stages of the mtSSU platform, decoding center, and the 3'-end of 12S rRNA. This process is governed by coordinated actions of assembly factors that ensure precise, stepwise rRNA folding and the integration of mitoribosomal proteins into the developing subunit. Our approach identifies pseudouridine synthase PUS1 and initiation factor mtIF2 as assembly factors, expanding their known roles beyond mt-tRNA maturation and translation, respectively. In addition, the identified assembly intermediates provide insight into the modular nature of mtSSU biogenesis in mitochondria and further link late-stage assembly to the acquisition of translational competence.
History
DepositionApr 21, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57668.png

Downloads & links

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Map

FileDownload / File: emd_57668.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 495.12 Å		0.83 Å/pix.
x 600 pix.
= 495.12 Å		0.83 Å/pix.
x 600 pix.
= 495.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8252 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.020382786 - 0.08392868
Average (Standard dev.)-0.000021610924 (±0.0027157012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 495.12003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_57668_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_57668_half_map_2.map
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Sample components

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Entire : mitoribosomal small subunit assembly intermediate

EntireName: mitoribosomal small subunit assembly intermediate
Components
  • Complex: mitoribosomal small subunit assembly intermediate

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Supramolecule #1: mitoribosomal small subunit assembly intermediate

SupramoleculeName: mitoribosomal small subunit assembly intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 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: EMDB MAP
EMDB ID:

15552
EMDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 30956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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