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- PDB-8qsj: Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qsj | |||||||||
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Title | Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 | |||||||||
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![]() | RIBOSOME / mitochondria / maturation / biogenesis / GTPBP7 / MTG1 / LSU | |||||||||
Function / homology | ![]() regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / rRNA methyltransferase activity / Respiratory electron transport / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / 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 / Glyoxylate metabolism and glycine degradation / mitochondrial fission / camera-type eye development / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial large ribosomal subunit / 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 / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / methyltransferase activity / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / cell junction / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / double-stranded DNA binding / endonuclease activity / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / synapse / calcium ion binding / regulation of DNA-templated transcription / nucleolus / GTP binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
![]() | Ritter, C. / Nguyen, T.G. / Kummer, E. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 238 KB | Display | |
Data in CIF | ![]() | 393.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17720MC ![]() 8pk0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() |
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#12: RNA chain | Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#48: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#55: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 43140.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() 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) ![]() |
-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) ![]() |
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#58: Protein | Mass: 37292.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 44 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PM8.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PM8.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/GNP.gif)
#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 |
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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: ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
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) |
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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 | ||||||||||||||||||||||||
Refine LS restraints |
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