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Outer dynein arms with a microtubule doublet in the presence of ADP.Vanadate
by subtomogram averaging, at 39 A resolution
#1: Surface view with section colored by density value, , Made by UCSF CHIMERA
#2: Surface view colored by height, , Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1697 |
|---|---|
| Authors | Movassagh T, Bui KH, Sakakibara H, Oiwa K, Ishikawa T |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, , Made by UCSF CHIMERA #2: Surface view colored by height, , 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 | Nat. Struct. Mol. Biol., Vol. 17, Issue 6, Page 761-7, Year 2010 |
|---|---|
| Title | Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis. |
| Authors | Tandis Movassagh, Khanh Huy Bui, Hitoshi Sakakibara, Kazuhiro Oiwa, Takashi Ishikawa Department of Biology, ETH Zurich, Zurich, Switzerland. |
| Keywords |  Adenosine Diphosphate (metabolism, 58-64-0), Adenosine Triphosphate (metabolism, 56-65-5), Algal Proteins (chemistry), Chlamydomonas reinhardtii (chemistry), Cryoelectron Microscopy, Dyneins (chemistry, 3.6.4.2), Electron Microscope Tomography, Flagella (chemistry), Imaging, Three-Dimensional, Models, Molecular, Molecular Motor Proteins (chemistry), Protein Conformation |
| Links | DOI: 10.1038/nsmb.1832, PubMed: 20453857 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1697.map ( map file in CCP4 format, 3264 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 = 876.8 A , B = 808.3 A , C = 369.9 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 6.85 A , Y = 6.85 A , Z = 6.85 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is an image of outer dynein arms with a microtubule doublet in the presence of ADP.Vanadate | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Outer dynein arm, microtubule doublet |
|---|---|
| Number of Components | 1 |
| Details | The sample was flagella in situ |
| Component #1: cellular-component - Outer dynein arm and Microtubule doublet | |
| Scientific name | Flagella |
| Common Name | Outer dynein arm and Microtubule doublet |
| Scientific Name of Species | Chlamydomonas reinhardtii (NCBI Taxonomy: 3055) |
| Common Name of Species | Green Algae |
| Recombinant expression | No |
| Natural Source | Organelle: Flagella Cell Location: Axoneme |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | 300 mesh lacey carbon grid |
|---|---|
| Specimen State | particle |
| Buffer | Details: 30 mM HEPES (pH 7.4), 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, 50 mM Potassium Acetate, 0.5% (w/v) Polyethylene Glycol (MW 20,000), 0.1 mM ATP with 0.05 mM sodium Orthovanadate pH: 7.4 |
| Vitrification | |
| Method | Blot for 3 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 95 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | FEI TECNAI 20 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 30 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Imaging Mode | BRIGHT FIELD |
| Energy Filter | Type: GIF , Window: 10-25 eV |
| Specimen Holder | |
| Holder | Eucentric Gatan cryo ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | -60 degrees - 60 degrees |
| Temperature | 100 Kelvin |
| Camera | |
| Detector | Gatan CCD |
| Image Acquisition | |
| Number of Digital Images | 1200 |
| Sampling Size | 6.85 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | subtomogram averaging |
|---|---|
| 3 D reconstruction | |
| Algorithm | Tomography |
| Software | IMOD |
| Resolution By Author | 39 |
| Resolution Method | FSC at 0.5 cut-off |
| Subtomogram Averaging | |
| Details | Average number of projections used in the 3D reconstructions: 6097. Average number of class averages: 2. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1697.xml (6.9 KB) | ||
|---|---|---|---|
| Map data | emd_1697.map.gz (2.7 MB) | ||
| Images |  1697ADPVi.jpg (74.6 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1697 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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