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Pretranslocation ribosome. Total population.
by single particle reconstruction, at 13 A resolution
#1: Surface view with section colored by density value, Surface level: 20, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 20, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1551 |
|---|---|
| Title | Pretranslocation ribosome. Total population. |
| Map | Pretranslocation ribosome |
| Sample | 70 mRNA tRNAfMet fMetLeu-tRNALeu |
| Keywords |  ribosome, pretranslocation, hybrid |
| Authors | Julian P, Konevega AL, Scheres SHW, Lazaro M, Gil D, Wintermeyer W, Rodnina MV, Valle M |
| Date | Deposition: 2008-09-08, Header release: 2008-09-15, Map release: 2009-05-05, Last update: 2012-10-24 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 20, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 20, 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 | Proc. Natl. Acad. Sci. U.S.A., Vol. 105, Issue 44, Page 16924-7, Year 2008 |
|---|---|
| Title | Structure of ratcheted ribosomes with tRNAs in hybrid states. |
| Authors | Patricia Julián, Andrey L Konevega, Sjors H W Scheres, Melisa Lázaro, David Gil, Wolfgang Wintermeyer, Marina V Rodnina, Mikel Valle Structural Biology Unit, Center for Cooperative Research in Biosciences bioGUNE, 48160 Derio, Spain. |
| Keywords | Cryoelectron Microscopy, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor G (chemistry), RNA, Transfer (chemistry, 9014-25-9), RNA, Transfer, Amino Acyl (chemistry), Ribosomes (chemistry), tRNA, peptidyl- |
| Links | DOI: 10.1073/pnas.0809587105, PubMed: 18971332, PMC: PMC2579354 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1551.map ( map file in CCP4 format, 16386 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 352 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.2 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Pretranslocation ribosome | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | 70 mRNA tRNAfMet fMetLeu-tRNALeu |
|---|---|
| Number of Components | 3 |
| Component #1: ribosome-prokaryote - pretranslocation ribosome | |
| Scientific name | 70S E.coli ribosome in the pretranslocation state |
| Common Name | pretranslocation ribosome |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Prokaryote | ALL |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Staining | cryoEM |
|---|---|
| Specimen Support Details | Quantifoil 300 mesh copper |
| Specimen State | particle |
| Buffer | Details: 50 mM Tris-HCl, pH 7.5 30mM KCl 70 mM NH4Cl 20 mM MgCl2 2 mM spermine pH: 7.5 |
| Vitrification | |
| Method | single blot for 1.5 seconds |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Temperature | 90 Kelvin |
| Imaging | |
| Microscope | OTHER |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 10 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | single tilt cryoholder |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 90 K |
| Camera | |
| Detector | CCD Gatan camera |
| Image Acquisition | |
| Sampling Size | 2.2 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | reference matching |
| Software | SPIDER XMIPP |
| CTF Correction | volume |
| Resolution By Author | 13 A |
| Resolution Method | FSC at 0.15 cut-off |
| Single Particle | |
| Number of Projections | 63539 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1551.xml (6.4 KB) | ||
|---|---|---|---|
| Map data | emd_1551.map.gz (14.6 MB) | ||
| Images |  emd_1551.jpg (59.7 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1551 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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