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Understanding Ribosome Assembly: The Structure of in vivo Assembled Immature 30S Subunits Revealed by Cryo-Electron Microscopy
by single particle reconstruction, at 11.6 A resolution
#1: Surface view with section colored by density value, Surface level: 1.97, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 1.97, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1774 |
|---|---|
| Title | Understanding Ribosome Assembly: The Structure of in vivo Assembled Immature 30S Subunits Revealed by Cryo-Electron Microscopy |
| Map | Surface rendering of the immature 30S ribosomal subunit from YjeQ-depleted E.coli cells. |
| Sample | Reconstruction of the immature 30S ribosomal subunit purified from yjeq-deficient E.coli strains. |
| Keywords |  3D Structure of Immature 30S Subunit |
| Authors | Jomaa A, Stewart G, Benito JM, Zielke R, Campbell T, Maddock J, Brown E, Ortega J |
| Date | Deposition: 2010-08-17, Header release: 2010-09-10, Map release: 2011-04-08, Last update: 2012-10-17 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.97, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 1.97, 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 | RNA, Vol. 17, Issue 4, Page 697-709, Year 2011 |
|---|---|
| Title | Understanding ribosome assembly: the structure of in vivo assembled immature 30S subunits revealed by cryo-electron microscopy. |
| Authors | Ahmad Jomaa, Geordie Stewart, Jaime Martín-Benito, Ryszard Zielke, Tracey L Campbell, Janine R Maddock, Eric D Brown, Joaquin Ortega Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N3Z5, Canada. |
| Keywords | Cryoelectron Microscopy, Escherichia coli (genetics), Escherichia coli Proteins (genetics), GTP Phosphohydrolases (genetics, 3.6.1.-), Gene Deletion, Protein Structure, Secondary, RNA, Ribosomal (chemistry), Ribosome Subunits, Small, Bacterial (chemistry), YjeQ protein, E coli (3.6.1.-) |
| Links | DOI: 10.1261/rna.2509811, PubMed: 21303937, PMC: PMC3062180 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1774.map ( map file in CCP4 format, 8390 KB ) | ||||||||||||||||||||||||
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| 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: 325.12 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.54 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Surface rendering of the immature 30S ribosomal subunit from YjeQ-depleted E.coli cells. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Reconstruction of the immature 30S ribosomal subunit purified from yjeq-deficient E.coli strains. |
|---|---|
| Number of Components | 1 |
| Theoretical Mass | 0.8MDa |
| Details | The sample was thawed from -80 degrees Celsius and diluted to a concentration of 58 nM. Sample was then applied on holey carbon grids with an additional thin layer of carbon (5-10 nm) and plunged in liquid ethane at liquid nitrogen temperature. |
| Component #1: ribosome-prokaryote - 30S | |
| Scientific name | Small Ribosomal Subunit |
| Common Name | 30S |
| Theoretical Mass | 0.85 MDa |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Prokaryote | SSU 30S |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 4.7 mg/ml |
|---|---|
| Specimen Support Details | 400 mesh Copper Grid |
| Specimen State | particle |
| Buffer | Details: 10 mM Tris-HCl, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol pH: 7.5 |
| Vitrification | |
| Method | Blot for 7 seconds twice before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: FEI vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Temperature | 93 Kelvin |
| Imaging | |
| Microscope | JEOL 2010F |
| Date | 16-OCT-2008 |
| 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: 50000 |
| Nominal Cs | 1 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 650 nm - 3900 nm |
| Specimen Holder | |
| Holder | Side entry Liquid Nitrogen-Cooled Cryo Specimen holder.This holder operates in the temperature range from -175 C to ambient. |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 93 K ( 93 - 93 K) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | NIKON SUPER COOLSCAN 9000 |
| Number of Digital Images | 72 |
| Sampling Size | 12.7 |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Projection Matching |
| Software | Xmipp |
| CTF Correction | Each Micrograph |
| Resolution By Author | 11.6 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 59054 |
| Details | Particles were picked using BOXER software implemented in EMAN. |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid Body |
| Software | Situs |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| PDB Entry ID | 2Z4K |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1774.xml (8 KB) | ||
|---|---|---|---|
| Map data | emd_1774.map.gz (7.4 MB) | ||
| Images |  EMD-1774.jpg (38.1 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1774 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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