[English] 日本語
![](img/lk-miru.gif)
- PDB-3bbx: The Hsp15 protein fitted into the low resolution Cryo-EM map of t... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3bbx | ||||||
---|---|---|---|---|---|---|---|
Title | The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex | ||||||
![]() |
| ||||||
![]() | RIBOSOME / ribosomal complex / large subunit / 50S rescue stalled ribosome | ||||||
Function / homology | ![]() 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 / translational initiation ...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 / 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 / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | ||||||
![]() | Jiang, L. / Abrahams, J.P. | ||||||
![]() | ![]() 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 |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 347.6 KB | Display | |
Data in CIF | ![]() | 494 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1455MC ![]() 1456C ![]() 3bbuC ![]() 3bbvC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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) ![]() ![]() |
---|---|
#2: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 28 types, 28 molecules VCDEFGHJKLMNOPQRSTUWXYZ01234
-Non-polymers , 2 types, 616 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#31: Chemical | ChemComp-MG / #32: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: 50S.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: ![]() |
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: 2AW4![]() 2aw4 Accession code: 2AW4 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
|