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Yorodumi- PDB-8csp: Human mitochondrial small subunit assembly intermediate (State A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8csp | |||||||||
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Title | Human mitochondrial small subunit assembly intermediate (State A) | |||||||||
Components |
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Keywords | RIBOSOME / Ribonucleoprotein complex / Mitochondria Biogenesis | |||||||||
Function / homology | Function and homology information : / rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / Mitochondrial Fatty Acid Beta-Oxidation / mitochondrial ribosome binding / rRNA (adenine-N6,N6-)-dimethyltransferase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity ...: / rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / Mitochondrial Fatty Acid Beta-Oxidation / mitochondrial ribosome binding / rRNA (adenine-N6,N6-)-dimethyltransferase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / S-adenosyl-L-methionine binding / mitochondrial small ribosomal subunit / regulation of cellular respiration / rRNA methylation / mitochondrial ribosome / fatty acid beta-oxidation / mitochondrial translation / mitochondrial nucleoid / ribosomal small subunit binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / apoptotic signaling pathway / Transcriptional activation of mitochondrial biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / fatty acid biosynthetic process / ribosomal small subunit assembly / regulation of translation / cell junction / small ribosomal subunit / methylation / nuclear membrane / cell population proliferation / tRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / mRNA binding / apoptotic process / GTP binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
Authors | Harper, N.J. / Burnside, C. / 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 | 8csp.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8csp.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8csp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/8csp ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8csp | HTTPS FTP |
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-Related structure data
Related structure data | 26966MC 8csqC 8csrC 8cssC 8cstC 8csuC 8d8jC 8d8kC 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
+28S ribosomal protein ... , 26 types, 26 molecules 01BCDEFGHJKLMNOPQRSTUVWXYZ
-Protein , 6 types, 6 molecules 45789a
#3: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
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#4: Protein | Mass: 39600.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q8WVM0, Transferases; Transferring one-carbon groups; Methyltransferases |
#5: Protein | Mass: 50807.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q9H7H0, Transferases; Transferring one-carbon groups; Methyltransferases |
#6: Protein | Mass: 43019.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q8IVS2, [acyl-carrier-protein] S-malonyltransferase |
#7: Protein | Mass: 78565.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NC60 |
#33: Protein | Mass: 48413.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75616 |
-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) Homo sapiens (human) / References: GenBank: 1858624182 |
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-Non-polymers , 8 types, 39 molecules
#34: Chemical | ChemComp-SF4 / | ||||||||||
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#35: Chemical | ChemComp-SAM / | ||||||||||
#36: Chemical | ChemComp-K / #37: Chemical | ChemComp-MG / #38: Chemical | #39: Chemical | ChemComp-ZN / | #40: Chemical | ChemComp-ATP / | #41: 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 |
-Sample preparation
Component | Name: Human mitochondrial small subunit assembly intermediate, State AMitochondrion Type: RIBOSOME / Entity ID: #1-#33 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R3.5/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: 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 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9109335 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 263184 Details: 12 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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