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- EMDB-12851: State D0'' of the human mitoribosomal large subunit assembly inte... -

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Basic information

Entry
Database: EMDB / ID: EMD-12851
TitleState D0'' of the human mitoribosomal large subunit assembly intermediate
Map data
SampleState D0'' of the human mitoribosomal large subunit assembly intermediate
Function / homology
Function and homology information


rRNA modification in the mitochondrion / negative regulation of mitochondrial translation / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / negative regulation of ribosome biogenesis / rRNA import into mitochondrion / RNA methylation / Respiratory electron transport / Mitochondrial translation elongation ...rRNA modification in the mitochondrion / negative regulation of mitochondrial translation / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / negative regulation of ribosome biogenesis / rRNA import into mitochondrion / RNA methylation / Respiratory electron transport / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / Mitochondrial translation initiation / mitochondrial translational termination / positive regulation of mitochondrial translation / translation release factor activity, codon nonspecific / mitochondrial translational elongation / protein targeting to mitochondrion / mitochondrial ribosome / mitochondrial small ribosomal subunit / camera-type eye development / protein lipoylation / mitochondrial respiratory chain complex I / acyl binding / aminoacyl-tRNA hydrolase / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / Glyoxylate metabolism and glycine degradation / mitochondrial respiratory chain complex I assembly / acyl carrier activity / mitochondrial electron transport, NADH to ubiquinone / aminoacyl-tRNA hydrolase activity / ribonuclease III activity / primary miRNA processing / mitochondrial translation / production of siRNA involved in RNA interference / pre-miRNA processing / mitochondrial large ribosomal subunit / ribosomal large subunit binding / rRNA methylation / regulation of cell cycle => GO:0051726 / RNA processing / anatomical structure morphogenesis / ribosomal large subunit biogenesis / fatty acid binding / cellular response to leukemia inhibitory factor / mitochondrial membrane / ribosome assembly / fibrillar center / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / fatty acid biosynthetic process / large ribosomal subunit / ribosomal large subunit assembly / Transferases; Transferring one-carbon groups; Methyltransferases / 5S rRNA binding / double-stranded RNA binding / ribosome biogenesis / methyltransferase activity / cell junction / ribonucleoprotein complex / double-stranded DNA binding / heart development / mitochondrial inner membrane / nuclear membrane / negative regulation of translation / ribosome / rRNA binding / nuclear body / structural constituent of ribosome / cell cycle / hydrolase activity / mitochondrial matrix / translation / mRNA binding / protein domain specific binding / nucleotide binding / apoptotic process / regulation of transcription, DNA-templated / nucleolus / calcium ion binding / viral process / mitochondrion / RNA binding / extracellular space / nucleoplasm / plasma membrane / nucleus / cytosol
Similarity search - Function
Mitochondrial termination factor repeats / MTERF superfamily, mitochondrial/chloroplastic / mTERF / Transcription termination factor, mitochondrial/chloroplastic / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / SAM-dependent methyltransferase RsmB/NOP2-type / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein S30, mitochondrial ...Mitochondrial termination factor repeats / MTERF superfamily, mitochondrial/chloroplastic / mTERF / Transcription termination factor, mitochondrial/chloroplastic / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / SAM-dependent methyltransferase RsmB/NOP2-type / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein S30, mitochondrial / Mitochondrial ribosomal protein L55 / Ribosomal protein L55, mitochondrial / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial 28S ribosomal protein S30 (PDCD9) / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Ribosomal protein L37, mitochondrial / Mitochondrial ribosome protein 63 / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal subunit / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitoribosomal protein mL52 / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L52, mitochondrial / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L53, mitochondrial / Tim44-like domain / Tim44-like domain / Tim44 / Ribosomal protein L35, mitochondrial / MRPL44, double-stranded RNA binding domain / Mitochondrial ribosomal protein L28 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L49/IMG2 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Mitochondrial ribosomal protein L27 / Ribosomal protein L27/L41, mitochondrial / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L46, N-terminal / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / TGS domain profile. / TGS / TGS-like / Complex 1 protein (LYR family) / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Complex 1 LYR protein / Ribonuclease III, endonuclease domain superfamily / RF-1 domain / Peptide chain release factor class I / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Acyl carrier protein (ACP) / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Beta-grasp domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / NTF2-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein L10-like domain superfamily / Phosphopantetheine attachment site / Ribosomal protein L10 / Ribosomal protein L10P / NUDIX hydrolase-like domain superfamily / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Nucleotidyltransferase superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, C-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9, N-terminal / Ribosomal protein L36 / Ribosomal protein L36
Similarity search - Domain/homology
39S ribosomal protein L44, mitochondrial / 39S ribosomal protein L34, mitochondrial / Ribosomal protein 63, mitochondrial / 39S ribosomal protein L45, mitochondrial / 39S ribosomal protein L32, mitochondrial / 39S ribosomal protein L20, mitochondrial / 39S ribosomal protein L13, mitochondrial / 39S ribosomal protein L9, mitochondrial / 39S ribosomal protein L4, mitochondrial / 39S ribosomal protein L37, mitochondrial ...39S ribosomal protein L44, mitochondrial / 39S ribosomal protein L34, mitochondrial / Ribosomal protein 63, mitochondrial / 39S ribosomal protein L45, mitochondrial / 39S ribosomal protein L32, mitochondrial / 39S ribosomal protein L20, mitochondrial / 39S ribosomal protein L13, mitochondrial / 39S ribosomal protein L9, mitochondrial / 39S ribosomal protein L4, mitochondrial / 39S ribosomal protein L37, mitochondrial / 39S ribosomal protein L18, mitochondrial / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L47, mitochondrial / 39S ribosomal protein L11, mitochondrial / 39S ribosomal protein S30, mitochondrial / 39S ribosomal protein L48, mitochondrial / 39S ribosomal protein L17, mitochondrial / 39S ribosomal protein S18a, mitochondrial / 39S ribosomal protein L22, mitochondrial / 39S ribosomal protein L16, mitochondrial / 39S ribosomal protein L39, mitochondrial / 39S ribosomal protein L35, mitochondrial / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L36, mitochondrial / 39S ribosomal protein L27, mitochondrial / 39S ribosomal protein L40, mitochondrial / 39S ribosomal protein L38, mitochondrial / 39S ribosomal protein L53, mitochondrial / 39S ribosomal protein L54, mitochondrial / MIEF1 upstream open reading frame protein / Acyl carrier protein, mitochondrial / 39S ribosomal protein L33, mitochondrial / 39S ribosomal protein L3, mitochondrial / 39S ribosomal protein L19, mitochondrial / 39S ribosomal protein L28, mitochondrial / 39S ribosomal protein L49, mitochondrial / Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L23, mitochondrial / 39S ribosomal protein L51, mitochondrial / 39S ribosomal protein L2, mitochondrial / 39S ribosomal protein L14, mitochondrial / Mitochondrial assembly of ribosomal large subunit protein 1 / 39S ribosomal protein L21, mitochondrial / Transcription termination factor 4, mitochondrial / 39S ribosomal protein L55, mitochondrial / 39S ribosomal protein L10, mitochondrial / 39S ribosomal protein L52, mitochondrial / 39S ribosomal protein L41, mitochondrial / 39S ribosomal protein L50, mitochondrial / 39S ribosomal protein L43, mitochondrial / Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L30, mitochondrial / 39S ribosomal protein L24, mitochondrial / 5-methylcytosine rRNA methyltransferase NSUN4 / 39S ribosomal protein L42, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLenarcic T / Jaskolowski M / Leibundgut M / Scaiola A / Schoenhut T / Saurer M / Lee RG / Rackham O / Filipovska A / Ban N
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182341 Switzerland
European Molecular Biology Organization (EMBO)1074-2019
Swiss National Science Foundation182880
CitationJournal: Nat Commun / Year: 2021
Title: Stepwise maturation of the peptidyl transferase region of human mitoribosomes.
Authors: Tea Lenarčič / Mateusz Jaskolowski / Marc Leibundgut / Alain Scaiola / Tanja Schönhut / Martin Saurer / Richard G Lee / Oliver Rackham / Aleksandra Filipovska / Nenad Ban /
Abstract: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral ...Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.
History
DepositionApr 30, 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: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12851.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 474.88 Å
1.06 Å/pix.
x 448 pix.
= 474.88 Å
1.06 Å/pix.
x 448 pix.
= 474.88 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
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.8602798 - 2.1715112
Average (Standard dev.)0.005818044 (±0.091339305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 474.87997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z474.880474.880474.880
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.8602.1720.006

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Supplemental data

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Sample components

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Entire State D0'' of the human mitoribosomal large subunit assembly inte...

EntireName: State D0'' of the human mitoribosomal large subunit assembly intermediate
Number of Components: 1

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Component #1: protein, State D0'' of the human mitoribosomal large subunit asse...

ProteinName: State D0'' of the human mitoribosomal large subunit assembly intermediate
Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HEK 293 EBNA

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: OTHER / Temperature: 277.15 K / Humidity: 100 %
Details: 4 uL of the sample was blotted for 2-6 sec before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 60 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 32871
3D reconstructionSoftware: cryoSPARC / Resolution: 3.5 Å / Resolution Method: FSC 0.143 CUT-OFF

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