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- PDB-8d8k: Yeast mitochondrial small subunit assembly intermediate (State 2) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d8k | |||||||||
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Title | Yeast mitochondrial small subunit assembly intermediate (State 2) | |||||||||
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![]() | RIBOSOME / Ribonucleoprotein complex / Mitochondria Biogenesis | |||||||||
Function / homology | ![]() mitochondrial translational initiation / Mitochondrial protein degradation / mitochondrial small ribosomal subunit / mitochondrial ribosome / sporulation resulting in formation of a cellular spore / mitochondrial translation / superoxide dismutase activity / RNA splicing / methyltransferase activity / mRNA processing ...mitochondrial translational initiation / Mitochondrial protein degradation / mitochondrial small ribosomal subunit / mitochondrial ribosome / sporulation resulting in formation of a cellular spore / mitochondrial translation / superoxide dismutase activity / RNA splicing / methyltransferase activity / mRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTP binding / mitochondrion / RNA binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
![]() | Burnside, C. / Harper, N.J. / 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 | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 196.7 KB | Display | |
Data in CIF | ![]() | 323.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27250MC ![]() 8cspC ![]() 8csqC ![]() 8csrC ![]() 8cssC ![]() 8cstC ![]() 8csuC ![]() 8d8jC ![]() 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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1 |
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Components
-Protein , 5 types, 5 molecules 0C2cL
#1: Protein | Mass: 72308.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P36056, Transferases; Transferring one-carbon groups; Methyltransferases |
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#3: Protein | Mass: 47170.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 15321.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 8017.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 16948.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+37S ribosomal protein ... , 27 types, 27 molecules 5MNOPQRSTUVWYZAB3D4EF6GHIJK
-Mitochondrial ... , 2 types, 2 molecules dX
#4: Protein | Mass: 101568.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#16: Protein | Mass: 12420.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 1 types, 1 molecules a
#31: RNA chain | Mass: 549234.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 4 types, 77 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/HOH.gif)
#36: Chemical | ChemComp-SF4 / | ||||
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#37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-ATP / | #39: Water | ChemComp-HOH / | |
-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: Yeast mitochondrial small subunit assembly intermediate (State 2) Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL |
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Molecular weight | Value: 1.22 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 | 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: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 61.73 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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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: 3286640 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54519 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5MRC |