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- EMDB-16409: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site... -

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Basic information

Entry
Database: EMDB / ID: EMD-16409
TitleHuman mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (masked refined on SSU tail)
Map dataLocal resolution filtered map masked refined on SSU tail, fitted
Sample
  • Complex: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site
Keywordsmitochondrial translation / mRNA delivery / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsSingh V / Itoh Y / Amunts A
Funding support Sweden, European Union, 5 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
European Research Council (ERC)European Union
European Molecular Biology Organization (EMBO)European Union
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.
Authors: Vivek Singh / J Conor Moran / Yuzuru Itoh / Iliana C Soto / Flavia Fontanesi / Mary Couvillion / Martijn A Huynen / L Stirling Churchman / Antoni Barrientos / Alexey Amunts /
Abstract: In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA ...In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA delivery factor and report its cryo-electron microscopy structure in complex with SLIRP (SRA stem-loop-interacting RNA-binding protein), mRNA and the mitoribosome. The structure shows that LRPPRC associates with the mitoribosomal proteins mS39 and the N terminus of mS31 through recognition of the LRPPRC helical repeats. Together, the proteins form a corridor for handoff of the mRNA. The mRNA is directly bound to SLIRP, which also has a stabilizing function for LRPPRC. To delineate the effect of LRPPRC on individual mitochondrial transcripts, we used RNA sequencing, metabolic labeling and mitoribosome profiling, which showed a transcript-specific influence on mRNA translation efficiency, with cytochrome c oxidase subunit 1 and 2 translation being the most affected. Our data suggest that LRPPRC-SLIRP acts in recruitment of mitochondrial mRNAs to modulate their translation. Collectively, the data define LRPPRC-SLIRP as a regulator of the mitochondrial gene expression system.
History
DepositionDec 29, 2022-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16409.png

Downloads & links

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Map

FileDownload / File: emd_16409.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map masked refined on SSU tail, fitted
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.13152102 - 0.25193065
Average (Standard dev.)-0.00018965702 (±0.0029176106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map masked refined on SSU tail, fitted

Fileemd_16409_additional_1.map
AnnotationUnsharpened map masked refined on SSU tail, fitted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: raw half map masked refined on SSU tail

Fileemd_16409_half_map_1.map
Annotationraw half map masked refined on SSU tail
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: raw half map masked refined on SSU tail

Fileemd_16409_half_map_2.map
Annotationraw half map masked refined on SSU tail
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 ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...

EntireName: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site
Components
  • Complex: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site

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Supramolecule #1: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...

SupramoleculeName: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNAs in the A-site, P-site and E-site
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6zm6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41815
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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