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- EMDB-15542: Human mitochondrial ribosome small subunit in complex with strept... -

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Basic information

Entry
Database: EMDB / ID: EMD-15542
TitleHuman mitochondrial ribosome small subunit in complex with streptomycin
Map dataSSU_body_masked_local_resolution_filtered
Sample
  • Complex: In vitro reconstituted complex of human mitochondrial ribosomal small subunit and streptomycin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsSingh V / Khawaja A / Itoh Y / Naschberger A / Rorbach J / Amunts A
Funding support Sweden, European Union, 5 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
H2020 Marie Curie Actions of the European CommissionEuropean Union
Swedish Research Council Sweden
European Molecular Biology Organization (EMBO)European Union
European Research Council (ERC)European Union
CitationJournal: Elife / Year: 2022
Title: Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
Authors: Yuzuru Itoh / Vivek Singh / Anas Khawaja / Andreas Naschberger / Minh Duc Nguyen / Joanna Rorbach / Alexey Amunts /
Abstract: The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was ...The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.
History
DepositionAug 5, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15542.png

Downloads & links

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Map

FileDownload / File: emd_15542.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSSU_body_masked_local_resolution_filtered
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.23525235 - 0.44226858
Average (Standard dev.)-3.3364548e-05 (±0.0051551834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15542_msk_1.map
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Additional map: #1

Fileemd_15542_additional_1.map
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Half map: #1

Fileemd_15542_half_map_1.map
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Half map: #2

Fileemd_15542_half_map_2.map
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Sample components

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Entire : In vitro reconstituted complex of human mitochondrial ribosomal s...

EntireName: In vitro reconstituted complex of human mitochondrial ribosomal small subunit and streptomycin
Components
  • Complex: In vitro reconstituted complex of human mitochondrial ribosomal small subunit and streptomycin

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Supramolecule #1: In vitro reconstituted complex of human mitochondrial ribosomal s...

SupramoleculeName: In vitro reconstituted complex of human mitochondrial ribosomal small subunit and streptomycin
type: complex / ID: 1 / Chimera: Yes / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 899952
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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