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Yorodumi- PDB-7o9k: Human mitochondrial ribosome large subunit assembly intermediate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o9k | ||||||
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Title | Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu | ||||||
Components |
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Keywords | RIBOSOME / Mitochondria / GTPase / Ribosome assembly intermediate | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Valentin Gese, G. / Hallberg, B.M. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7o9k.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7o9k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7o9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o9k_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7o9k_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7o9k_validation.xml.gz | 225.4 KB | Display | |
Data in CIF | 7o9k_validation.cif.gz | 361.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/7o9k ftp://data.pdbj.org/pub/pdb/validation_reports/o9/7o9k | HTTPS FTP |
-Related structure data
Related structure data | 12763MC 7o9mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+39S ribosomal protein ... , 47 types, 53 molecules 0a123456789DEFFFt1t2t3t4t5t6HIJKLMNOQ...
-RNA chain , 2 types, 2 molecules AB
#12: RNA chain | Mass: 500033.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#14: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021 |
-Protein , 9 types, 9 molecules A1A2nopqtvw
#13: Protein | Mass: 43140.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q96CB9, Transferases; Transferring one-carbon groups; Methyltransferases |
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#15: Protein | Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z6M4 |
#53: Protein | Mass: 27464.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q9UI43, Transferases; Transferring one-carbon groups; Methyltransferases |
#54: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#55: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#56: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#59: Protein | Mass: 49613.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49411 |
#61: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#62: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
-Mitochondrial ... , 4 types, 4 molecules CGPu
#16: Protein | Mass: 37292.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BT17 |
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#21: Protein | Mass: 45015.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTG2, GTPBP5, OBGH1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9H4K7 |
#30: Protein | Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K9D2 |
#60: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3 |
-Protein/peptide , 1 types, 1 molecules UNK
#63: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Non-polymers , 7 types, 101 molecules
#64: Chemical | #65: Chemical | ChemComp-MG / #66: Chemical | ChemComp-SAM / | #67: Chemical | #68: Chemical | ChemComp-GTP / | #69: Chemical | ChemComp-SAH / | #70: Chemical | ChemComp-PNS / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 55S subunit assembly intermediate / Type: RIBOSOME Details: Assembly intermediate of the human mitochondrial ribosome large subunit Entity ID: #1-#63 / Source: NATURAL |
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Molecular weight | Value: 1.5 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 20 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
-Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39495 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %
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