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- PDB-8csu: Human mitochondrial small subunit assembly intermediate (State C*) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8csu | |||||||||
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Title | Human mitochondrial small subunit assembly intermediate (State C*) | |||||||||
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![]() | RIBOSOME / Ribonucleoprotein complex / Mitochondria Biogenesis | |||||||||
Function / homology | ![]() mitochondrial DNA-directed RNA polymerase complex / rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination ...mitochondrial DNA-directed RNA polymerase complex / rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / S-adenosyl-L-methionine binding / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / rRNA methylation / mitochondrial ribosome / mitochondrial translation / mitochondrial nucleoid / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / apoptotic signaling pathway / Transcriptional activation of mitochondrial biogenesis / rRNA processing / cell junction / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / methylation / nuclear membrane / cytosolic small ribosomal subunit / cell population proliferation / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
![]() | Harper, N.J. / Burnside, C. / Klinge, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Principles of mitoribosomal small subunit assembly in eukaryotes. Authors: Nathan J Harper / Chloe Burnside / Sebastian Klinge / ![]() Abstract: Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is ...Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism. Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 174 KB | Display | |
Data in CIF | ![]() | 279.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26971MC ![]() 8cspC ![]() 8csqC ![]() 8csrC ![]() 8cssC ![]() 8cstC ![]() 8d8jC ![]() 8d8kC ![]() 8d8lC 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
+28S ribosomal protein ... , 27 types, 27 molecules 01BCDEFGHIJKLMNOPQRSTUVWXYZ
-Protein , 5 types, 5 molecules 34567
#3: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#4: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 39600.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q8WVM0, Transferases; Transferring one-carbon groups; Methyltransferases |
#6: Protein | Mass: 38417.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 50807.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q9H7H0, Transferases; Transferring one-carbon groups; Methyltransferases |
-RNA chain , 1 types, 1 molecules A
#8: RNA chain | Mass: 306449.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 9 types, 39 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
#34: Chemical | ChemComp-SF4 / | ||||||||||||
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#35: Chemical | ChemComp-SAM / | ||||||||||||
#36: Chemical | ChemComp-K / #37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-NAD / | #39: Chemical | ChemComp-ZN / | #40: Chemical | #41: Chemical | ChemComp-ATP / | #42: Chemical | ChemComp-GDP / | |
-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 mitochondrial small subunit assembly intermediate, State C* Type: RIBOSOME / Entity ID: #1-#33 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 47037 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9109335 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33642 Details: 11 focused maps calculated in RELION 3.1.1 were combined into a composite map using phenix.combine_focused_maps. Composite half maps were generated by combining each half map from focused refinements. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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