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Yorodumi- PDB-3bbx: The Hsp15 protein fitted into the low resolution Cryo-EM map of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bbx | ||||||
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Title | The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex | ||||||
Components |
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Keywords | RIBOSOME / ribosomal complex / large subunit / 50S rescue stalled ribosome | ||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / 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 / mRNA regulatory element binding translation repressor activity ...negative regulation of cytoplasmic translational initiation / 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 / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | ||||||
Authors | Jiang, L. / Abrahams, J.P. | ||||||
Citation | Journal: J Mol Biol / Year: 2009 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3bbx.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3bbx.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 3bbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bbx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3bbx_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3bbx_validation.xml.gz | 347.6 KB | Display | |
Data in CIF | 3bbx_validation.cif.gz | 494 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbx ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbx | HTTPS FTP |
-Related structure data
Related structure data | 1455MC 1456C 3bbuC 3bbvC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357928 |
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#2: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357927 |
+50S ribosomal protein ... , 28 types, 28 molecules VCDEFGHJKLMNOPQRSTUWXYZ01234
-Non-polymers , 2 types, 616 molecules
#31: Chemical | ChemComp-MG / #32: Water | ChemComp-HOH / | |
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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: 50S.nc-tRNA.Hsp15 complex / Type: COMPLEX |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3.5 nm / Nominal defocus min: 1.5 nm / Cs: 2 mm |
Image recording | Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF correction of each particle | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: cross-common lines, projection matching / Resolution: 10 Å / Nominal pixel size: 2.54 Å / Actual pixel size: 2.54 Å / Details: EMAN software / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: best visual fit, best correlation value Details: METHOD--colores REFINEMENT PROTOCOL--multi-rigid body refinement | ||||||||||||
Atomic model building | PDB-ID: 2AW4 2aw4 Accession code: 2AW4 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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