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Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15.
by single particle reconstruction, at 10 A resolution
#1: Surface view with section colored by density value, Surface level: 1.603128647, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 1.603128647, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1456 |
|---|---|
| Title | Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15. |
| Map | EM map of 50S.nc-tRNA.Hsp15 |
| Sample | 50S E.coli ribosomal subunit in complex with nascent chain-tRNA and Hsp15 |
| Authors | Jiang L, Schaffitzel C, Bingel-Erlenmeyer R, Ban N, Korber P, Koning RI, Plaisier JR, Abrahams JP |
| Date | Deposition: 2007-11-09, Header release: 2007-11-09, Map release: 2008-11-24, Last update: 2012-09-19 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.603128647, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 1.603128647, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Mol. Biol., Vol. 386, Issue 5, Page 1357-67, 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 Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. |
| Keywords |  Cryoelectron Microscopy, DNA-Binding Proteins (chemistry), Escherichia coli Proteins (chemistry), Heat-Shock Proteins (chemistry), Models, Molecular, Puromycin (chemistry, 53-79-2), RNA, Bacterial (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosome Subunits, Large, Bacterial (chemistry), hslR protein, E coli |
| Links | PII: S0022-2836(08)01371-5, DOI: 10.1016/j.jmb.2008.10.079, PubMed: 19013177 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1456.map ( map file in CCP4 format, 8389 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 325.12 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.54 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | EM map of 50S.nc-tRNA.Hsp15 | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | 50S E.coli ribosomal subunit in complex with nascent chain-tRNA and Hsp15 |
|---|---|
| Number of Components | 3 |
| Theoretical Mass | 1.6MDa |
| Component #1: ribosome-prokaryote - 50S ribosomal subunit | |
| Scientific name | 50S ribosomal subunit |
| Experimental Mass | 1.6 MDa |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Prokaryote | LSU 50S |
| Recombinant expression | No |
| Component #2: nucleic-acid - nascent chain-tRNA | |
| Scientific name | nascent chain-tRNA |
| Experimental Mass | 0.03 MDa |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Class | T-RNA |
| Structure | SINGLE STRANDED |
| Synthetic | No |
| Component #3: protein - Heat Shock Protein 15 | |
| Scientific name | Heat Shock Protein 15 |
| Experimental Mass | 0.015 MDa |
| Oligomeric Details | Mono |
| Number of Copies | 1 |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Vitrification | |
| Cryogen Name | ETHANE |
| Imaging | |
| Microscope | FEI TECNAI 20 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Illumination Mode | OTHER |
| Lens | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Model | OTHER |
| Camera | |
| Image Acquisition | |
| Number of Digital Images | 112 |
| Quant Bit Number | 8 |
| Scanner | OTHER |
| Details | Nikon super coolscan 9000 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Common lines |
| Software | EMAN |
| CTF Correction | Each particle |
| Resolution By Author | 10 A |
| Resolution Method | FSC at 0.5 cut-off |
| Euler Angles Details | EMAN:angle ~4 degrees |
| Details | Final maps were calculated by "refine" subprogram |
| Atomic Model Fitting | |
| Model #0 | |
| Refinement Protocol | rigid body |
| Target Criteria | R-factor |
| Software | Situs, LocalFit |
| Details | Protocol: multi-rigid body refinement. The domains were separately fitted manually, then optimized by Situs and LocalFit |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1456.xml (7.3 KB) | ||
|---|---|---|---|
| Map data | emd_1456.map.gz (828 KB) | ||
| Images |  1456.gif (59.4 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1456 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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