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The single particle reconstruction of the human Toll-like receptor 5 ectodomain in detergent
by single particle reconstruction, at 26 A resolution
#1: Surface view with section colored by density value, Surface level: 3.57, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 3.57, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5288 |
|---|---|
| Title | The single particle reconstruction of the human Toll-like receptor 5 ectodomain in detergent |
| Map | This is the volume of the hTLR5 ectodomain. |
| Sample | toll-like receptor 5 ectodomain |
| Keywords |  Toll-like receptor 5, ectodomain |
| Authors | Zhou K, Kanai R, Lee P, Wang HW, Modis Y |
| Date | Deposition: 2011-05-02, Header release: 2011-05-05, Map release: 2011-12-19, Last update: 2011-12-19 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 3.57, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 3.57, 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 | J. Struct. Biol., Vol. 177, Issue 2, Page 402-9, Year 2012 |
|---|---|
| Title | Toll-like receptor 5 forms asymmetric dimers in the absence of flagellin. |
| Authors | Kaifeng Zhou, Ryuta Kanai, Phong Lee, Hong-Wei Wang, Yorgo Modis Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA. |
| Keywords | Flagellin (chemistry, 12777-81-0), Glycosylation, Humans, Models, Molecular, Particle Size, Protein Binding, Protein Interaction Domains and Motifs, Protein Multimerization, Protein Processing, Post-Translational, Protein Structure, Quaternary, Structural Homology, Protein, Surface Properties, TLR5 protein, human, Toll-Like Receptor 5 (chemistry) |
| Links | PII: S1047-8477(11)00348-0, DOI: 10.1016/j.jsb.2011.12.002, PubMed: 22173220 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5288.map ( map file in CCP4 format, 4002 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 = 214 A , B = 214 A , C = 214 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.14 A , Y = 2.14 A , Z = 2.14 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is the volume of the hTLR5 ectodomain. | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | toll-like receptor 5 ectodomain |
|---|---|
| Number of Components | 2 |
| Oligomeric State | dimer |
| Theoretical Mass | 0.2 MDa |
| Details | The sample was monodisperse |
| Mass-estimation Method | gel filtration |
| Experimental Mass | 0.2 MDa |
| Component #1: protein - TLR5 | |
| Scientific name | Toll-like receptor |
| Common Name | TLR5 |
| Theoretical Mass | 0.2 MDa |
| Experimental Mass | 0.2 MDa |
| Oligomeric Details | dimer |
| Number of Copies | 2 |
| Scientific Name of Species | Homo sapiens (NCBI Taxonomy: 9606) |
| Common Name of Species | Human |
| Recombinant expression | Yes |
| Natural Source | Cell: Sf9 insect cells Organelle: membrane Cell Location: plasma membrane |
| Engineered Source | Vector: pAcGP67-A Exp System: Sf9 insect cells |
| Links | InterPro: IPR:017241 |
 Experiment | |
| Sample Preparation | |
| Staining | The protein solution was applied onto a thin-carbon-covered holey carbon copper grid and negatively stained in 1% uranyl-formate solution for 1 minute. |
|---|---|
| Specimen Conc | 0.005 mg/ml |
| Specimen Support Details | thin carbon covered home-made holey carbon on 400 mesh copper grid |
| Specimen State | particle |
| Buffer | Details: 10 mM TEA, 0.15 M NaCl pH: 7.5 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI 12 |
| Date | 01-AUG-2010 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 52000 X, Calibrated: 52000 X |
| Nominal Cs | 2.2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 800 nm - 1200 nm |
| Specimen Holder | |
| Holder | Eucentric ( SIDE ENTRY, EUCENTRIC ) |
| Camera | |
| Detector | Gatan Ultra4000 |
| Image Acquisition | |
| Number of Digital Images | 50 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Random conical tilt followed by projection matching refinement |
| Software | IMAGIC SPIDER |
| Details | Final maps were calculated from all the particles by back-projection reconstruction. |
| Resolution By Author | 26 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Class Averages | 100 |
| Number of Projections | 3087 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5288.xml (7.4 KB) | ||
|---|---|---|---|
| Map data | emd_5288.map.gz (3.4 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5288 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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