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Structure of the E. coli signal recognition particle bound to a translating ribosome.
by single particle reconstruction, at 20 A resolution
#1: Surface view with section colored by density value, Surface level: 0.25, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 0.25, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-2iy3, Surface level: 0.25, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-2iy3, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1251 |
|---|---|
| Title | Structure of the E. coli signal recognition particle bound to a translating ribosome. |
| Map | This is the map file of the E. coli signal recognition particle bound to a non-translating ribosome. |
| Sample | E. coli ribosome and signal recognition particle |
| Authors | Schaffitzel C, Oswald M, Berger I, Ishikawa T, Abrahams JP, Koerten HK, Koning RI, Ban N |
| Date | Deposition: 2006-07-29, Header release: 2006-07-29, Map release: 2008-07-29, 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: 0.25, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 0.25, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2iy3, Surface level: 0.25, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-2iy3, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Nature, Vol. 444, Issue 7118, Page 503-6, Year 2006 |
|---|---|
| Title | Structure of the E. coli signal recognition particle bound to a translating ribosome. |
| Authors | Christiane Schaffitzel, Miro Oswald, Imre Berger, Takashi Ishikawa, Jan Pieter Abrahams, Henk K Koerten, Roman I Koning, Nenad Ban ETH Zurich, Institute for Molecular Biology and Biophysics, HPK Building, Schafmattstrasse 20, 8093 Zurich, Switzerland. |
| Keywords |  Base Sequence, Binding Sites, Escherichia coli (genetics), Membrane Proteins (biosynthesis), Models, Molecular, Molecular Sequence Data, Protein Biosynthesis, RNA (chemistry, 63231-63-0), RNA, Ribosomal (chemistry), Ribosomes (chemistry), Signal Recognition Particle (chemistry) |
| Links | DOI: 10.1038/nature05182, PubMed: 17086205 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1251.map ( map file in CCP4 format, 5325 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: 419.1 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 3.81 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is the map file of the E. coli signal recognition particle bound to a non-translating ribosome. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | E. coli ribosome and signal recognition particle |
|---|---|
| Oligomeric State | One SRP binds to one ribosome. |
| Number of Components | 2 |
| Component #1: ribosome-prokaryote - E.coli 70S ribosome | |
| Scientific name | E.coli 70S ribosome |
| Theoretical Mass | 2.5 MDa |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Prokaryote | ALL |
| Recombinant expression | No |
| Component #2: ligand - Signal rocognition particle | |
| Scientific name | E.coli SRP |
| Common Name | Signal rocognition particle |
| Theoretical Mass | 0.09 MDa |
| Oligomeric Details | monomer |
| Number of Copies | 1 |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Recombinant expression | Yes |
| Natural Source | Cell Location: cytosol |
| Engineered Source | Vector: pET24a_Ffh and pUC19_Ffs NCBI taxonomy: 469008 Expression system: Escherichia coli BL21(DE3) |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 0.375 mg/ml |
|---|---|
| Specimen Support Details | carbon-coated lacey formvar grids |
| Specimen State | particle |
| Buffer | Details: 50mM Hepes-KOH pH7.5,100mM KCl,25mM MgCl2,1mM DTT,1mM GTP pH: 7.5 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Humidity | 100 |
| Temperature | 298 Kelvin |
| Instrument | HOMEMADE PLUNGER |
| Method | blot for 1.5 sec before plunging |
| Details | Vitrification instrument: home-built environmental chamber and vitrification device |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 10 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000, Calibrated: 51000 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 4500 nm |
| Specimen Holder | |
| Holder | cryo stage |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
| Detector | Kodak SO163 |
| Image Acquisition | |
| Number of Digital Images | 212 |
| Scanner | OTHER |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Software | spider |
| Resolution By Author | 20 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 9300 |
| Atomic Model Fitting | |
| Fitted Coordinate | |
| PDB entry ID | |
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