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- EMDB-1455: Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Com... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1455 | |||||||||
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Title | Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15. | |||||||||
![]() | EM map of 50S.nc-tRNA complex | |||||||||
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Function / homology | ![]() negative regulation of cytoplasmic translational initiation / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...negative regulation of cytoplasmic translational initiation / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / cellular response to heat / large ribosomal subunit rRNA binding / 5S rRNA binding / response to heat / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / single-stranded RNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
![]() | Jiang L / Schaffitzel C / Bingel-Erlenmeyer R / Ban N / Korber P / Koning RI / Plaisier JR / Abrahams JP | |||||||||
![]() | ![]() Title: Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15. Authors: Linhua Jiang / Christiane Schaffitzel / Rouven Bingel-Erlenmeyer / Nenad Ban / Philipp Korber / Roman I Koning / Daniël C de Geus / Jasper R Plaisier / Jan Pieter Abrahams / ![]() Abstract: When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain ...When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain that remains threaded through the exit tunnel. Hsp15, a highly upregulated bacterial heat shock protein, reactivates such dead-end complexes. Here, we show with cryo-electron microscopy reconstructions and functional assays that Hsp15 translocates the tRNA moiety from the A site to the P site of stalled 50S subunits. By stabilizing the tRNA in the P site, Hsp15 indirectly frees up the A site, allowing a release factor to land there and cleave off the tRNA. Such a release factor must be stop codon independent, suggesting a possible role for a poorly characterized class of putative release factors that are upregulated by cellular stress, lack a codon recognition domain and are conserved in eukaryotes. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 879.5 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.2 KB 9.2 KB | Display Display | ![]() |
Images | ![]() | 32.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 298.3 KB | Display | ![]() |
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Full document | ![]() | 297.9 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bbuMC ![]() 3bbvMC ![]() 3bbxMC ![]() 1456C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM map of 50S.nc-tRNA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 50S E.coli ribosomal subunit in complex with nascent chain-tRNA
Entire | Name: 50S E.coli ribosomal subunit in complex with nascent chain-tRNA |
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Components |
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-Supramolecule #1000: 50S E.coli ribosomal subunit in complex with nascent chain-tRNA
Supramolecule | Name: 50S E.coli ribosomal subunit in complex with nascent chain-tRNA type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Theoretical: 1.6 MDa |
-Supramolecule #1: 50S ribosomal subunit
Supramolecule | Name: 50S ribosomal subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 1.6 MDa |
-Macromolecule #1: nascent chain-tRNA
Macromolecule | Name: nascent chain-tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 30 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Digitization - Scanner: OTHER / Number real images: 42 / Details: Nikon super coolscan 9000 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Details: Final maps were calculated by "refine" subprogram |
Final angle assignment | Details: EMAN:angle ~4 degrees |
-Atomic model buiding 1
Software | Name: Situs, LocalFit |
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Details | Protocol: multi-rigid body refinement. The domains were separately fitted manually, then optimized by Situs and LocalFit |
Refinement | Protocol: RIGID BODY FIT / Target criteria: R-factor |
Output model | ![]() PDB-3bbu: ![]() PDB-3bbv: ![]() PDB-3bbx: |