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- EMDB-13963: Cryo-EM structure of the human mtLSU assembly intermediate upon M... -

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Basic information

Entry
Database: EMDB / ID: EMD-13963
TitleCryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 3
Map data
Sample
  • Complex: Human mitochondrial ribosome large subunit
KeywordsMitochondria / Ribosome / Assembly / Methyltransferase / MRM2 / RNA modification
Function / homology
Function and homology information


negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / Complex I biogenesis / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / Respiratory electron transport / rRNA import into mitochondrion ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / Complex I biogenesis / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / Respiratory electron transport / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / translation release factor activity / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / mitochondrial translation / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / ribosomal large subunit binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / RNA processing / rescue of stalled ribosome / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / aerobic respiration / ribosomal large subunit biogenesis / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / 5S rRNA binding / small ribosomal subunit rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / mitochondrial matrix / protein domain specific binding / translation / ribonucleoprotein complex / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein S30, mitochondrial / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / Ribosomal protein L51, mitochondrial ...MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein S30, mitochondrial / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L37/S30 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / : / : / Mitochondrial 28S ribosomal protein S30 (PDCD9) / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / MRPL44, double-stranded RNA binding domain / : / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / Large ribosomal subunit protein bL9m C-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / : / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Beta-grasp domain superfamily / Acyl carrier protein (ACP) / NTF2-like domain superfamily / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Ribosomal protein L28/L24 superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily
Similarity search - Domain/homology
Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL51 ...Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL38 / Mitochondrial assembly of ribosomal large subunit protein 1 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL66 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsRebelo-Guiomar P / Pellegrino S / Dent KC / Warren AJ / Minczuk M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/4 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.
Authors: Pedro Rebelo-Guiomar / Simone Pellegrino / Kyle C Dent / Aldema Sas-Chen / Leonor Miller-Fleming / Caterina Garone / Lindsey Van Haute / Jack F Rogan / Adam Dinan / Andrew E Firth / Byron ...Authors: Pedro Rebelo-Guiomar / Simone Pellegrino / Kyle C Dent / Aldema Sas-Chen / Leonor Miller-Fleming / Caterina Garone / Lindsey Van Haute / Jack F Rogan / Adam Dinan / Andrew E Firth / Byron Andrews / Alexander J Whitworth / Schraga Schwartz / Alan J Warren / Michal Minczuk /
Abstract: Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that ...Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent. MRM2 controls mitochondrial respiration by regulating mitoribosome biogenesis. In its absence, mtLSU particles (visualized by cryo-EM at the resolution of 2.6 Å) present disordered RNA domains, partial occupancy of bL36m and bound MALSU1:L0R8F8:mtACP anti-association module, allowing five mtLSU biogenesis intermediates with different intersubunit interface configurations to be placed along the assembly pathway. However, mitoribosome biogenesis does not depend on the methyltransferase activity of MRM2. Disruption of the MRM2 Drosophila melanogaster orthologue leads to mitochondria-related developmental arrest. This work identifies a key checkpoint during mtLSU assembly, essential to maintain mitochondrial homeostasis.
History
DepositionDec 10, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13963.png

Downloads & links

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Map

FileDownload / File: emd_13963.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.015687142 - 0.062883094
Average (Standard dev.)-0.000071054026 (±0.003534481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z381.600381.600381.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0160.063-0.000

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Supplemental data

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Sample components

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Entire : Human mitochondrial ribosome large subunit

EntireName: Human mitochondrial ribosome large subunit
Components
  • Complex: Human mitochondrial ribosome large subunit

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Supramolecule #1: Human mitochondrial ribosome large subunit

SupramoleculeName: Human mitochondrial ribosome large subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#49
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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 52.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2709521
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 748427
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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