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Yorodumi- EMDB-12768: Human mitochondrial ribosome large subunit assembly intermediate ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12768 | |||||||||
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Title | Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-TU (mtEF-Tu-loaded subset) | |||||||||
Map data | Main map produced in CryoSPARC homogeneous refienement | |||||||||
Sample |
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Function / homology | Function and homology information regulation of respiratory system process / rRNA modification in the mitochondrion / SARS-CoV-2 modulates autophagy / regulation of mitochondrial translation / rRNA 2'-O-methylation / tRNA (cytidine-5-)-methyltransferase activity / 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 / rRNA modification in the mitochondrion / SARS-CoV-2 modulates autophagy / regulation of mitochondrial translation / rRNA 2'-O-methylation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / RNA methylation / rRNA methyltransferase activity / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / protein targeting to mitochondrion / mitochondrial fission / camera-type eye development / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / rRNA methylation / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / mitochondrial nucleoid / ribosomal large subunit binding / translational elongation / acyl binding / anatomical structure morphogenesis / Complex I biogenesis / acyl carrier activity / Respiratory electron transport / translation elongation factor activity / RNA processing / mitochondrial respiratory chain complex I assembly / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / : / ribosomal large subunit biogenesis / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / cellular response to leukemia inhibitory factor / methyltransferase activity / Mitochondrial protein degradation / fatty acid binding / mitochondrial membrane / aerobic respiration / fibrillar center / fatty acid biosynthetic process / rRNA processing / cell junction / large ribosomal subunit / double-stranded RNA binding / ribosome biogenesis / double-stranded DNA binding / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / response to ethanol / cytosolic large ribosomal subunit / mitochondrial outer membrane / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / synapse / calcium ion binding / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Valentin Gese G / Hallberg BM | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12768.map.gz | 52.1 MB | EMDB map data format | |
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Header (meta data) | emd-12768-v30.xml emd-12768.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12768_fsc.xml | 20.8 KB | Display | FSC data file |
Images | emd_12768.png | 75.9 KB | ||
Others | emd_12768_half_map_1.map.gz emd_12768_half_map_2.map.gz | 52.1 MB 52.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12768 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12768 | HTTPS FTP |
-Validation report
Summary document | emd_12768_validation.pdf.gz | 609.8 KB | Display | EMDB validaton report |
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Full document | emd_12768_full_validation.pdf.gz | 608.9 KB | Display | |
Data in XML | emd_12768_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_12768_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12768 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12768 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12768.map.gz / Format: CCP4 / Size: 56.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Main map produced in CryoSPARC homogeneous refienement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map B
File | emd_12768_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_12768_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 55S subunit assembly intermediate
Entire | Name: 55S subunit assembly intermediate |
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Components |
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-Supramolecule #1: 55S subunit assembly intermediate
Supramolecule | Name: 55S subunit assembly intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#63 Details: Assembly intermediate of the human mitochondrial ribosome large subunit |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |