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Yorodumi- PDB-8qsj: Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qsj | |||||||||
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Title | Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 | |||||||||
Components |
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Keywords | RIBOSOME / mitochondria / maturation / biogenesis / GTPBP7 / MTG1 / LSU | |||||||||
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 / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis ...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 / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / rRNA methyltransferase activity / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / iron-sulfur cluster assembly complex / protein targeting to mitochondrion / mitochondrial large ribosomal subunit binding / mitochondrial fission / camera-type eye development / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / rRNA methylation / [2Fe-2S] cluster assembly / aminoacyl-tRNA hydrolase activity / respiratory chain complex I / mitochondrial ribosome / iron-sulfur cluster assembly / mitochondrial translation / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / heart development / large ribosomal subunit rRNA binding / double-stranded DNA binding / 5S rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / synapse / GTP binding / regulation of DNA-templated transcription / nucleolus / 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 Å | |||||||||
Authors | Ritter, C. / Nguyen, T.G. / Kummer, E. | |||||||||
Funding support | Denmark, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome. Authors: Thu Giang Nguyen / Christina Ritter / Eva Kummer / Abstract: Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ...Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qsj.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qsj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qsj_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8qsj_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8qsj_validation.xml.gz | 238 KB | Display | |
Data in CIF | 8qsj_validation.cif.gz | 393.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/8qsj ftp://data.pdbj.org/pub/pdb/validation_reports/qs/8qsj | HTTPS FTP |
-Related structure data
Related structure data | 17720MC 8pk0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+39S ribosomal protein ... , 46 types, 46 molecules 0123456789DEFHIJKLMNOPQRSTUVWX...
-RNA chain , 2 types, 2 molecules AB
#11: RNA chain | Mass: 512186.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...) ...Details: Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...),Unidentified RNA sequence at 3' end modelled as AUAUAU(...) Source: (natural) Homo sapiens (human) / References: GenBank: 1530720620 |
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#12: RNA chain | Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1896813692 |
-Protein , 8 types, 8 molecules bopqvwxy
#36: Protein | Mass: 23352.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983 |
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#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 |
#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 |
#54: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#55: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
#56: 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 |
#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 |
-Mitochondrial ... , 2 types, 2 molecules uz
#53: 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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#58: 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 , 6 types, 44 molecules
#59: Chemical | #60: Chemical | ChemComp-MG / #61: Chemical | ChemComp-FES / | #62: Chemical | ChemComp-PM8 / | #63: Chemical | ChemComp-SAM / | #64: Chemical | ChemComp-GNP / | |
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-Details
Has ligand of interest | Y |
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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 2 with GTPBP7 Type: RIBOSOME / Entity ID: #1-#15, #17, #16, #18-#35, #37-#58 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.6 |
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 / Nominal defocus max: 2800 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68901 / Symmetry type: POINT | ||||||||||||||||||||||||
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