[English] 日本語
Yorodumi- PDB-3bbv: The tRNA(phe) fitted into the low resolution Cryo-EM map of the 5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bbv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The tRNA(phe) fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex | |||||||||
Components | tRNA(Phe) | |||||||||
Keywords | RIBOSOME / PHE / tRNA / rescue stalled ribosome | |||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3bbv.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bbv.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 3bbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bbv_validation.pdf.gz | 647.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3bbv_full_validation.pdf.gz | 676.1 KB | Display | |
Data in XML | 3bbv_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3bbv_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbv ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbv | HTTPS FTP |
-Related structure data
Related structure data | 1455MC 1456C 3bbuC 3bbxC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: RNA chain | Mass: 24649.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: part of the 50S ribosomal particle in assembly with Heat Shock Protein 15 Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 0S.nc-tRNA.Hsp15 complex / Type: COMPLEX |
---|---|
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 |
---|---|
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 |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 2OW8 2ow8 Pdb chain-ID: z / Accession code: 2OW8 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
|