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Yorodumi- PDB-8d8k: Yeast mitochondrial small subunit assembly intermediate (State 2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d8k | |||||||||
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Title | Yeast mitochondrial small subunit assembly intermediate (State 2) | |||||||||
Components |
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Keywords | RIBOSOME / Ribonucleoprotein complex / Mitochondria Biogenesis | |||||||||
Function / homology | Function and homology information mitochondrial translational initiation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding ...mitochondrial translational initiation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / methylation / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTP binding / mitochondrion / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Burnside, C. / Harper, N.J. / Klinge, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d8k.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8d8k.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8d8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/8d8k ftp://data.pdbj.org/pub/pdb/validation_reports/d8/8d8k | HTTPS FTP |
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-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 (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
-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) Saccharomyces cerevisiae (brewer's yeast) 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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02381 |
#21: Protein | Mass: 15321.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38783 |
#34: Protein | Mass: 8017.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#35: Protein | Mass: 16948.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q5F6 |
+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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4FBQ6 |
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#16: Protein | Mass: 12420.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53305 |
-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) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1887067169 |
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-Non-polymers , 4 types, 77 molecules
#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 |
-Sample preparation
Component | Name: Yeast mitochondrial small subunit assembly intermediate (State 2)Mitochondrion Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL |
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Molecular weight | Value: 1.22 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
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 FIELDBright-field microscopy / 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) |
-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 |