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- EMDB-12767: Human mitochondrial ribosome large subunit assembly intermediate ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12767
TitleHuman mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-TU (MTG1-loaded subset)
Map dataMain map produced in CryoSPARC homogeneous refinement
Sample
  • Complex: 55S subunit assembly intermediate
Function / homology
Function and homology information


regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / SARS-CoV-2 modulates autophagy / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity ...regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / SARS-CoV-2 modulates autophagy / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA methyltransferase activity / Respiratory electron transport / RNA methylation / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / protein targeting to mitochondrion / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / camera-type eye development / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / rRNA methylation / acyl binding / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / iron-sulfur cluster assembly / acyl carrier activity / translational elongation / mitochondrial translation / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / ribosomal large subunit binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / anatomical structure morphogenesis / RNA processing / translation elongation factor activity / rescue of stalled ribosome / aerobic respiration / ribosomal large subunit biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / small ribosomal subunit rRNA binding / fibrillar center / rRNA processing / fatty acid biosynthetic process / large ribosomal subunit rRNA binding / double-stranded RNA binding / large ribosomal subunit / ribosome biogenesis / cell junction / heart development / double-stranded DNA binding / endonuclease activity / response to ethanol / mitochondrial inner membrane / mitochondrial outer membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / GTPase activity / synapse / apoptotic process / calcium ion binding / GTP binding / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / mitochondrion
Similarity search - Function
GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / OBG-type GTPase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic ...GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / OBG-type GTPase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF / MIEF1-MP, LYR domain / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal RNA large subunit methyltransferase E / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Ribosomal protein L37, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L46 NUDIX / 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 L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Tim44-like domain / Ribosomal protein L7/L12 dimerisation domain / Tim44 / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / 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 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / PEBP-like superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / 50S ribosome-binding GTPase / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / GTP binding domain / Double stranded RNA-binding domain (dsRBD) profile. / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Mitochondrial ribosomal protein L18, isoform CRA_b / Large ribosomal subunit protein uL22m / 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 / Elongation factor Tu, mitochondrial / Large ribosomal subunit protein bL12m / Large ribosomal subunit protein bL28m ...Mitochondrial ribosomal protein L18, isoform CRA_b / Large ribosomal subunit protein uL22m / 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 / Elongation factor Tu, mitochondrial / Large ribosomal subunit protein bL12m / 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 / Transcription termination factor 4, mitochondrial / 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 / 5-methylcytosine rRNA methyltransferase NSUN4 / 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 / Mitochondrial ribosome-associated GTPase 1 / 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 mL46 / Mitochondrial ribosome-associated GTPase 2 / 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 uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / rRNA methyltransferase 2, mitochondrial / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsValentin Gese G / Hallberg BM
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for late maturation steps of the human mitoribosomal large subunit.
Authors: Miriam Cipullo / Genís Valentín Gesé / Anas Khawaja / B Martin Hällberg / Joanna Rorbach /
Abstract: Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. ...Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation.
History
DepositionApr 19, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12767.png

Downloads & links

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Map

FileDownload / File: emd_12767.map.gz / Format: CCP4 / Size: 56.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map produced in CryoSPARC homogeneous refinement
Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.42353716 - 1.3855659
Average (Standard dev.)0.043369707 (±0.14340578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin138187187
Dimensions276246217
Spacing217276246
CellA: 221.34 Å / B: 281.52 Å / C: 250.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z217276246
origin x/y/z0.0000.0000.000
length x/y/z221.340281.520250.920
α/β/γ90.00090.00090.000
start NX/NY/NZ187138187
NX/NY/NZ217276246
MAP C/R/S321
start NC/NR/NS187138187
NC/NR/NS246276217
D min/max/mean-0.4241.3860.043

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Supplemental data

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Half map: Half map B

Fileemd_12767_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_12767_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 55S subunit assembly intermediate

EntireName: 55S subunit assembly intermediate
Components
  • Complex: 55S subunit assembly intermediate

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Supramolecule #1: 55S subunit assembly intermediate

SupramoleculeName: 55S subunit assembly intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#63
Details: Assembly intermediate of the human mitochondrial ribosome large subunit
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.5 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

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 21609
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ool

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT

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