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Cryo-electron tomography averaged map of microtubule doublet 3 in the proximal region of Chlamydomonas axoneme
by subtomogram averaging, at 41.5 A resolution
#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 1, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2124 |
|---|---|
| Authors | Bui KH, Yagi T, Yamamoto R, Kamiya R, Ishikawa T |
| 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, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1, 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. Cell Biol., Vol. 198, Issue 5, Page 913-25, Year 2012 |
|---|---|
| Title | Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme. |
| Authors | Khanh Huy Bui, Toshiki Yagi, Ryosuke Yamamoto, Ritsu Kamiya, Takashi Ishikawa Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland. |
| Keywords |  Chlamydomonas (chemistry), Dyneins (chemistry, 3.6.4.2), Flagella (chemistry), Microtubules (chemistry), Plant Cells (chemistry), Plant Proteins (chemistry) |
| Links | DOI: 10.1083/jcb.201201120, PubMed: 22945936, PMC: PMC3432765 |
 Map | |||||||||||||||||||||||||
| File |  EMD-2124.map ( map file in CCP4 format, 32002 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 = 1450.0 A , B = 1450.0 A , C = 1450.0 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 7.25 A , Y = 7.25 A , Z = 7.25 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Reconstruction of outer doublet 3 of the Chlamydomonas axoneme in the proximal region. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Outer doublet 3 of Chlamydomonas axoneme in the proximal region |
|---|---|
| Number of Components | 1 |
| Details | Flagella were isolated from Chlamydomonas. |
| Component #1: cellular-component - axoneme, cilia | |
| Scientific name | flagellum |
| Common Name | axoneme, cilia |
| Scientific Name of Species | Chlamydomonas reinhardtii (NCBI Taxonomy: 3055) |
| Common Name of Species | green algae |
| Strain | c137 (mt+) |
| Recombinant expression | No |
| Natural Source | Organelle: flagella Cell Location: proximal part of the flagellum |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 2 mg/ml |
|---|---|
| Specimen Support Details | 300 mesh Quantifoil Holey Carbon copper grid R2/1 |
| Buffer | Details: 30 mM Hepes, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl, and 0.5% (wt/vol) polyethylene glycol (MW 20,000) pH: 7.4 |
| Vitrification | |
| Method | Offset -3, blot 3 seconds, drain time 0 second |
| Cryogen Name | ETHANE |
| Humidity | 90 |
| Instrument | FEI VITROBOT MARK II |
| Temperature | 110 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI 20 |
| Date | 26-NOV-2010 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 60 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 27500 X, Calibrated: 19303 X |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 4000 nm - 6000 nm |
| Energy Filter | Type: Gatan Tridem , Window: 0-20 eV |
| Specimen Holder | |
| Holder | Gatan 626, liquid nitrogen cooled ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | -60 degrees - 60 degrees |
| Temperature | 98 Kelvin ( 93 Kelvin - 118 Kelvin ) |
| Camera | |
| Detector | Gatan Ultrascan 1000 FT CCD |
| Image Acquisition | |
| Number of Digital Images | 493 |
| Quant Bit Number | 16 |
 Processing | |
| Method | subtomogram averaging |
|---|---|
| 3 D reconstruction | |
| Algorithm | subtomogram averaging |
| Software | IMOD, BSOFT, SPIDER, TOM, package, Matlab |
| Resolution By Author | 41.5 |
| Resolution Method | FSC at 0.5 cut-off |
| Subtomogram Averaging | |
| Details | R-weighted back projection using IMOD with fiducial markers. Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-2124.xml (7.7 KB) | ||
|---|---|---|---|
| Map data | emd_2124.map.gz (25.1 MB) | ||
| Images |  emd_2124.png (193.1 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2124 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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