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Structure of the E. coli protein-conducting channel bound to a translating ribosome.
by single particle reconstruction, at 14.9 A resolution
#1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-2akh, PDB-2aki, PDB-2gyb, PDB-2gyc, Surface level: 50, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-2akh, Made by Jmol
#5: Simplified surface model with fitted atomic model: PDB-2aki, Made by Jmol
#6: Simplified surface model with fitted atomic model: PDB-2gyb, Made by Jmol
#7: Simplified surface model with fitted atomic model: PDB-2gyc, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1143 |
|---|---|
| Authors | Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks III CL, Ban N, Frank J |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2akh, PDB-2aki, PDB-2gyb, PDB-2gyc, Surface level: 50, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-2akh, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-2aki, Made by Jmol #6: Simplified surface model with fitted atomic model: PDB-2gyb, Made by Jmol #7: Simplified surface model with fitted atomic model: PDB-2gyc, 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. 438, Issue 7066, Page 318-24, Year 2005 |
|---|---|
| Title | Structure of the E. coli protein-conducting channel bound to a translating ribosome. |
| Authors | Kakoli Mitra, Christiane Schaffitzel, Tanvir Shaikh, Florence Tama, Simon Jenni, Charles L Brooks, Nenad Ban, Joachim Frank Howard Hughes Medical Institute, Health Research Inc. at the Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA. |
| Keywords |  Cell Membrane (chemistry), Cryoelectron Microscopy, Escherichia coli Proteins (biosynthesis), Membrane Proteins (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Pliability, Protein Binding, Protein Biosynthesis, Protein Structure, Quaternary, Protein Transport, Ribosomes (metabolism), SecE protein, E coli, SecG protein, E coli, SecY protein, E coli |
| Links | DOI: 10.1038/nature04133, PubMed: 16292303, PMC: PMC1351281 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1143.map ( map file in CCP4 format, 7087 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 = 341.22 A , B = 341.22 A , C = 341.22 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing |
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| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | EM map of the E.coli proten-conducting channel bound to a translating ribosome | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | co-translational E. coli 70S ribosome-nascent chain complexed with SecYEG |
|---|---|
| Number of Components | 8 |
| Component #1: ribosome-prokaryote - small subunit | |
| Scientific name | 30S |
| Common Name | small subunit |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562)
|
| Prokaryote | SSU 30S |
| Recombinant expression | No |
| Component #2: ribosome-prokaryote - large subunit | |
| Scientific name | 50S |
| Common Name | large subunit |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562) |
| Prokaryote | LSU 50S |
| Recombinant expression | No |
| Component #3: nucleic-acid - A-site tRNA | |
| Scientific name | A-site tRNA |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562) |
| Synthetic | No |
| Structure | DOUBLE HELIX |
| Class | RNA |
| Component #4: nucleic-acid - P-site tRNA | |
| Scientific name | P-site tRNA |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562) |
| Synthetic | No |
| Structure | DOUBLE HELIX |
| Class | RNA |
| Component #5: nucleic-acid - E-site tRNA | |
| Scientific name | E-site tRNA |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562) |
| Structure | DOUBLE HELIX |
| Class | RNA |
| Synthetic | No |
| Component #6: nucleic-acid - mRNA | |
| Scientific name | mRNA |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562) |
| Structure | SINGLE STRANDED |
| Class | RNA |
| Synthetic | Yes |
| Component #7: protein - translocon, SecYEG | |
| Scientific name | protein-conducting channel |
| Common Name | translocon, SecYEG |
| Oligomeric Details | dimer of heterotrimer |
| Number of Copies | 2 |
| Scientific Name of Species | Escherichia coli (NCBI Taxonomy: 562) |
| Common Name of Species | translocon |
| Recombinant expression | Yes |
| Natural Source | Cell Location: inner membrane |
| Engineered Source | Exp System: Escherichia coli (NCBI Taxonomy: 562) |
| Component #8: protein - nascent chain | |
| Scientific name | nascent chain |
| Details | Strep-II-FtsQ-SecM construct |
| Scientific Name of Species | unidentified (NCBI Taxonomy: 32644) |
| Common Name of Species | translocon |
| Recombinant expression | Yes |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Vitrification | |
| Cryogen Name | ETHANE |
| Humidity | 90 |
| Temperature | 93 Kelvin |
| Instrument | HOMEMADE PLUNGER |
| Method | Blot for 2 seconds before plunging |
| Details | Vitrification instrument: two sided blotting plunger |
| Imaging | |
| Microscope | FEI TECNAI F30 |
| Date | 2004-03-09 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 11 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 39000 X, Calibrated: 39000 X |
| Nominal Cs | 2.26 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1500 nm - 4300 nm |
| Specimen Holder | |
| Holder | Cryo stage ( OTHER ) |
| Temperature | 93 Kelvin |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Number of Digital Images | 385 |
| Sampling Size | 14 microns |
| Od Range | 1.2 |
| Quant Bit Number | 12 |
| Scanner | ZEISS SCAI |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | reference projection |
| Software | SPIDER package |
| CTF Correction | defocus groups |
| Resolution By Author | 14.9 |
| Resolution Method | FSC at 0.5 cut-off |
| Euler Angles Details | SPIDER: theta 15 degrees, phi 15 degrees |
| Details | The falloff of Fourier amplitudes toward higher spatial frequencies was corrected using the x-ray solution scattering intensity distribution of 70S ribosomes from E. coli during each round of refinement |
| Single Particle | |
| Number of Projections | 53325 |
| Atomic Model Fitting | |
| Model #0 | |
| Refinement Protocol | flexible |
| Target Criteria | correlation coefficient |
| Refinement Space | REAL |
| Details | Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels |
| Model #1 | |
| Refinement Protocol | flexible |
| Target Criteria | correlation coefficient |
| Refinement Space | REAL |
| Details | Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels |
| Model #2 | |
| Refinement Protocol | rigid body |
| Target Criteria | R-factor |
| Software | RSR2000 |
| Refinement Space | REAL |
| Details | Protocol: real space refinement |
| Model #3 | |
| Refinement Protocol | rigid body |
| Target Criteria | R-factor |
| Software | RSR2000 |
| Refinement Space | REAL |
| Details | Protocol: real space refinement |
| Fitted Coordinate | |
| PDB entry ID | |
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