3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
High-resolution Cryo-EM structure of a programmed wheat germ ribosome
by single particle reconstruction, at 5.5 A resolution
#1: Surface view with section colored by density value, Surface level: 0.11, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 0.11, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3iz6, PDB-3iz7, PDB-3iz9, PDB-3izr, Surface level: 0.11, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-3iz6, Made by Jmol
#5: Simplified surface model with fitted atomic model: PDB-3iz7, Made by Jmol
#6: Simplified surface model with fitted atomic model: PDB-3iz9, Made by Jmol
#7: Simplified surface model with fitted atomic model: PDB-3izr, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1780 |
|---|---|
| Authors | Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, Soeding J, Westhof E, Wilson DN, Beckmann R |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.11, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 0.11, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3iz6, PDB-3iz7, PDB-3iz9, PDB-3izr, Surface level: 0.11, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-3iz6, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-3iz7, Made by Jmol #6: Simplified surface model with fitted atomic model: PDB-3iz9, Made by Jmol #7: Simplified surface model with fitted atomic model: PDB-3izr, 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 Fit?: input model of fitting or unreleased data (?) |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Map | |||||||||||||||||||||||||
| File |  EMD-1780.map ( map file in CCP4 format, 199346 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A = 455.4 A , B = 455.4 A , C = 455.4 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.2375 A , Y = 1.2375 A , Z = 1.2375 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Cryo-EM map of a programmed wheat germ ribosome containing a P-site tRNA | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Programmed Wheat Germ 80S Ribosome |
|---|---|
| Number of Components | 1 |
| Oligomeric State | One Ribosome |
| Theoretical Mass | 4.2 MDa |
| Mass-estimation Method | Sedimentation |
| Experimental Mass | 4.2 MDa |
| Component #1: ribosome-eukaryote - Wheat Germ Ribosome | |
| Scientific name | Tritcum aestivum 80S ribosome |
| Common Name | Wheat Germ Ribosome |
| Theoretical Mass | 4.2 MDa |
| Experimental Mass | 4.2 MDa |
| Scientific Name of Species | Triticum aestivum (NCBI Taxonomy: 4565)
|
| Common Name of Species | Bread wheat |
| Eukaryote | ALL |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Staining | Cryo-EM |
|---|---|
| Specimen Conc | 0.02 mg/ml |
| Specimen Support Details | Quantifoil Grid with 2 nm carbon on top |
| Specimen State | particle |
| Buffer | Details: 20 mM HEPES/KOH, pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.01 mg/ml cycloheximide, 1 mM DTT, 0.01 % Nikkol pH: 7.5 |
| Vitrification | |
| Method | Blot for 10 seconds before plunging, use 2 layers of filter paper |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | FEI TECNAI F30 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 25 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 39000 X, Calibrated: 38900 X |
| Nominal Cs | 2.26 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 4500 nm |
| Specimen Holder | |
| Holder | FEI Polara Cartridge System ( OTHER ) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Od Range | 1.2 |
| Scanner | PRIMESCAN |
| Number of Digital Images | 1374 |
| Sampling Size | 4.76 microns |
| Quant Bit Number | 16 |
| Details | Scanned at 5334 dpi on a Heidelberg Primescan Drum Scanner |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection Matching |
| Software | SPIDER |
| CTF Correction | Wiener Filter on 3D volumes (SPIDER) |
| Resolution By Author | 5.5 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | The reconstruction contains 2108230 particles in total |
| Fitted Coordinate | |
| PDB entry ID | |
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - EMDB-1780
Article
Cryoelectron Microscopy
Z (Sec.)
X (Row.)
Y (Col.)
1780_wg_bf030_front.png (958.4 KB)
Contact