[English] 日本語
Yorodumi- PDB-8csu: Human mitochondrial small subunit assembly intermediate (State C*) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8csu | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human mitochondrial small subunit assembly intermediate (State C*) | |||||||||
Components |
| |||||||||
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 ribosome binding / rRNA (adenine-N6,N6-)-dimethyltransferase activity / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination ...rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / mitochondrial ribosome binding / rRNA (adenine-N6,N6-)-dimethyltransferase activity / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / apoptotic signaling pathway / Transcriptional activation of mitochondrial biogenesis / ribosomal small subunit biogenesis / rRNA processing / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / 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 / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
Authors | Harper, N.J. / Burnside, C. / Klinge, S. | |||||||||
Funding support | United States, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8csu.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8csu.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8csu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/8csu ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8csu | 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 (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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) Homo sapiens (human) / References: UniProt: Q9NWT8 |
---|---|
#4: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
#5: 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 |
#6: Protein | Mass: 38417.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N0V3 |
#7: 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 |
-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 |
---|
-Non-polymers , 9 types, 39 molecules
#34: Chemical | ChemComp-SF4 / | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#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 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human mitochondrial small subunit assembly intermediate, State C*Mitochondrion Type: RIBOSOME / Entity ID: #1-#33 / Source: NATURAL |
---|---|
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 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|