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- EMDB-18461: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-18461
Titlemt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
Map datamt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
Sample
  • Complex: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
KeywordsMitochondria / Assembly / GTPBP8 / RIBOSOME
Function / homology
Function and homology information


negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / negative regulation of ribosome biogenesis / Complex I 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 / negative regulation of ribosome biogenesis / Complex I 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 / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / 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 / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / mitochondrial translation / [2Fe-2S] cluster assembly / 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 / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / aerobic respiration / cellular response to leukemia inhibitory factor / fatty acid binding / ribosomal large subunit biogenesis / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / nucleolus / structural molecule activity / 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 L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial ...MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L28 / 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 / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / 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 L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / 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 / NTF2-like domain superfamily / Acyl carrier protein (ACP) / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Phosphopantetheine attachment site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain
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 mL54 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL55 / Large ribosomal subunit protein uL10m / 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 mL53 / Large ribosomal subunit protein mL48 / 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 mL46 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL40 / 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 uL11m / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsValentin Gese G / Cipullo M / Rorbach J / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: GTPBP8 plays a role in mitoribosome formation in human mitochondria.
Authors: Miriam Cipullo / Genís Valentín Gesé / Shreekara Gopalakrishna / Annika Krueger / Vivian Lobo / Maria A Pirozhkova / James Marks / Petra Páleníková / Dmitrii Shiriaev / Yong Liu / ...Authors: Miriam Cipullo / Genís Valentín Gesé / Shreekara Gopalakrishna / Annika Krueger / Vivian Lobo / Maria A Pirozhkova / James Marks / Petra Páleníková / Dmitrii Shiriaev / Yong Liu / Jelena Misic / Yu Cai / Minh Duc Nguyen / Abubakar Abdelbagi / Xinping Li / Michal Minczuk / Markus Hafner / Daniel Benhalevy / Aishe A Sarshad / Ilian Atanassov / B Martin Hällberg / Joanna Rorbach /
Abstract: Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these ...Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.
History
DepositionSep 15, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18461.png

Downloads & links

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Map

FileDownload / File: emd_18461.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 600 pix.
= 606. Å		1.01 Å/pix.
x 600 pix.
= 606. Å		1.01 Å/pix.
x 600 pix.
= 606. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1290596 - 3.1285477
Average (Standard dev.)-0.00074139563 (±0.06451419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 606.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18461_msk_1.map
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Half map: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state...

Fileemd_18461_half_map_1.map
Annotationmt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2, half map A
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Half map: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state...

Fileemd_18461_half_map_2.map
Annotationmt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2, half map B
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Sample components

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Entire : mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2

EntireName: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
Components
  • Complex: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2

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Supramolecule #1: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2

SupramoleculeName: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.7 MDa

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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

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Electron microscopy

MicroscopeFEI TITAN 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: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 404181
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 76769
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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