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Yorodumi- PDB-7pd3: Structure of the human mitoribosomal large subunit in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 7pd3 | |||||||||
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Title | Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP | |||||||||
Components |
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Keywords | RIBOSOME / mitochondrial ribosome / large subunit / ribosome biogenesis / GTPase / rRNA modification | |||||||||
Function / homology | Function and homology information regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / 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 / ribosomal large subunit binding / acyl binding / anatomical structure morphogenesis / Complex I biogenesis / acyl carrier activity / Respiratory electron transport / 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 / double-stranded RNA binding / double-stranded DNA binding / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / 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 / regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Chandrasekaran, V. / Desai, N. / Burton, N.O. / Yang, H. / Price, J. / Miska, E.A. / Ramakrishnan, V. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Elife / Year: 2021 Title: Visualizing formation of the active site in the mitochondrial ribosome. Authors: Viswanathan Chandrasekaran / Nirupa Desai / Nicholas O Burton / Hanting Yang / Jon Price / Eric A Miska / V Ramakrishnan / Abstract: Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved ...Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis. | |||||||||
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 | 7pd3.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pd3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pd3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7pd3_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7pd3_validation.xml.gz | 225.2 KB | Display | |
Data in CIF | 7pd3_validation.cif.gz | 356.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/7pd3 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pd3 | HTTPS FTP |
-Related structure data
Related structure data | 13329MC 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, 48 molecules 0123456789CHDEFGJKLMNOPQRSTUVW...
-RNA chain , 2 types, 2 molecules AB
#11: RNA chain | Mass: 500070.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#12: 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 , 7 types, 7 molecules opqvwyx
#48: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
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#49: 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 |
#50: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#55: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#56: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
#57: Protein | Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z6M4 |
#58: 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 |
-Protein/peptide , 1 types, 1 molecules t
#53: 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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-Mitochondrial ... , 2 types, 2 molecules uz
#54: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3 |
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#59: Protein | Mass: 37292.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BT17 |
-Non-polymers , 11 types, 275 molecules
#60: Chemical | #61: Chemical | ChemComp-A / #62: Chemical | ChemComp-U / #63: Chemical | ChemComp-C / #64: Chemical | ChemComp-OMG / | #65: Chemical | ChemComp-G / #66: Chemical | ChemComp-PSU / | #67: Chemical | ChemComp-MG / #68: Chemical | ChemComp-PNS / | #69: Chemical | ChemComp-SAM / | #70: Chemical | |
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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: human mitoribosomal large subunit assembly intermediate Type: RIBOSOME / Entity ID: #1-#59 / Source: NATURAL |
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Molecular weight | 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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.1 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66340 / Symmetry type: POINT |