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- EMDB-19958: Human mitochondrial RNase Z with tRNA-His-CCA, consensus map -

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Basic information

Entry
Database: EMDB / ID: EMD-19958
TitleHuman mitochondrial RNase Z with tRNA-His-CCA, consensus map
Map dataHuman mitochondrial RNAseZ with tRNA-His-CCA, consensus map
Sample
  • Complex: RNAseZ with mt-tRNA-His
KeywordsRNAseZ / ELAC2 / mitochondria / tRNA / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsValentin Gese G / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO J / Year: 2024
Title: Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex.
Authors: Genís Valentín Gesé / B Martin Hällberg /
Abstract: Maturation of human mitochondrial tRNA is essential for cellular energy production, yet the underlying mechanisms remain only partially understood. Here, we present several cryo-EM structures of the ...Maturation of human mitochondrial tRNA is essential for cellular energy production, yet the underlying mechanisms remain only partially understood. Here, we present several cryo-EM structures of the mitochondrial RNase Z complex (ELAC2/SDR5C1/TRMT10C) bound to different maturation states of mitochondrial tRNA, showing the molecular basis for tRNA-substrate selection and catalysis. Our structural insights provide a molecular rationale for the 5'-to-3' tRNA processing order in mitochondria, the 3'-CCA antideterminant effect, and the basis for sequence-independent recognition of mitochondrial tRNA substrates. Furthermore, our study links mutations in ELAC2 to clinically relevant mitochondrial diseases, offering a deeper understanding of the molecular defects contributing to these conditions.
History
DepositionMar 26, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19958.png

Downloads & links

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Map

FileDownload / File: emd_19958.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 600 pix.
= 420.16 Å		0.7 Å/pix.
x 600 pix.
= 420.16 Å		0.7 Å/pix.
x 600 pix.
= 420.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.70027 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.013580796 - 0.033240188
Average (Standard dev.)-0.0000019906647 (±0.0017463509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 420.16022 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19958_msk_1.map
Projections & Slices
AxesZYX

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Half map: Human mitochondrial RNAseZ with tRNA-His-CCA, consensus half map...

Fileemd_19958_half_map_1.map
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, consensus half map 1 unfiltered
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human mitochondrial RNAseZ with tRNA-His-CCA, consensus half map...

Fileemd_19958_half_map_2.map
AnnotationHuman mitochondrial RNAseZ with tRNA-His-CCA, consensus half map 2 unfiltered
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNAseZ with mt-tRNA-His

EntireName: RNAseZ with mt-tRNA-His
Components
  • Complex: RNAseZ with mt-tRNA-His

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Supramolecule #1: RNAseZ with mt-tRNA-His

SupramoleculeName: RNAseZ with mt-tRNA-His / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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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: 48.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4773315
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4436
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta-1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7onu

source_name: PDB, initial_model_type: experimental model

bq52

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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