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Structure of a type III secretion needle
by helical reconstruction, at 7.7 A resolution
#1: Surface view with section colored by density value, Surface level: 6.76, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 6.76, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Made by UCSF CHIMERA
#4: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5352 |
|---|---|
| Title | Structure of a type III secretion needle |
| Map | This is an reconstruction of the type III secretion needle |
| Sample | Shigella needle |
| Keywords |  type III secretion system, needle, helical filament |
| Authors | Fujii T, Cheung M, Blanco A, Kato T, Blocker AJ, Namba K |
| Date | Deposition: 2011-11-02, Header release: 2011-11-28, Map release: 2012-02-20, Last update: 2012-03-06 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 6.76, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 6.76, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Made by UCSF CHIMERA #4: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, 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 Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Proc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 12, Page 4461-6, Year 2012 |
|---|---|
| Title | Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms. |
| Authors | Takashi Fujii, Martin Cheung, Amandine Blanco, Takayuki Kato, Ariel J Blocker, Keiichi Namba Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan. |
| Keywords | Bacterial Proteins (chemistry), Calibration, Cell Membrane (metabolism), Cryoelectron Microscopy (methods), Image Processing, Computer-Assisted, Models, Molecular, Molecular Conformation, MxiH protein, Shigella, Polymers (chemistry), Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Shigella flexneri (metabolism), Signal Transduction, Temperature |
| Links | DOI: 10.1073/pnas.1116126109, PubMed: 22388746, PMC: PMC3311390 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5352.map ( map file in CCP4 format, 4002 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 = 168.0 A , B = 168.0 A , C = 168.0 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.68 A , Y = 1.68 A , Z = 1.68 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is an reconstruction of the type III secretion needle | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Shigella needle |
|---|---|
| Number of Components | 1 |
| Oligomeric State | helical assembly of MxiH |
| Component #1: protein - MxiH | |
| Scientific name | MxiH |
| Scientific Name of Species | Shigella flexneri (NCBI Taxonomy: 623) |
| Recombinant expression | Yes |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Delta Z: 4.30 A Delta Phi: 64.06 degrees Hand: RIGHT HANDED |
|---|---|
| Specimen State | filament |
| Buffer | pH: 7.4 Details: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4 |
| Vitrification | |
| Method | Blot for 3.5 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | JEOL 3200FSC |
| Date | 02-JUL-2008 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, Calibrated: 89285 X |
| Nominal Cs | 1.6 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 2000 nm |
| Energy Filter | Type: JEOL Omega filter , Window: 0-10 eV |
| Specimen Holder | |
| Holder | top entry ( OTHER ) |
| Temperature | 50 Kelvin ( 50 Kelvin - 60 Kelvin ) |
| Camera | |
| Detector | TemCam-F415MP |
| Image Acquisition | |
| Number of Digital Images | 330 |
| Sampling Size | 15 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection Matching |
| Software | SPIDER |
| CTF Correction | CTFFIND3 Each particle |
| Resolution By Author | 7.7 |
| Resolution Method | FSC at 0.5 cut-off |
| Fitted Coordinate | |
| PDB entry ID | |
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