|Entry||Database: EMDB / ID: 1787|
|Title||Asymmetric reconstruction of doublecortin-stabilised microtubules decorated with kinesin motor domain|
|Keywords||Tubulin / MAP / microtubule / stabilisation / doublecortin / kinesin|
|Sample||Microtubules co-polymerised with doublecortin and bound with kinesin motor domain|
|Source||Bos taurus / mammal / Bovine / Cattle (Wikipedia) / |
Homo sapiens / human / Wikipedia
Rattus norvegicus / mammal / Rat / Brown rat (Wikipedia) /
|Map data||This is a C1 reconstruction of doublecortin-stabilised microtubule decorated with kinesin motor domain|
|Method||single particle reconstruction, at 13.5 Å resolution|
|Authors||Fourniol FJ / Sindelar CV / Amigues B / Clare D / Thomas G / Perderiset M / Francis F / Houdusse A / Moores CA|
|Citation||J. Cell Biol., 2010, 191, 463-470|
|Date||Deposition: Sep 15, 2010 / Header (metadata) release: Sep 24, 2010 / Map release: Oct 29, 2010 / Last update: Sep 19, 2012|
Downloads & links
|File||emd_1787.map.gz (map file in CCP4 format, 39367 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.8 Å|
CCP4 map header:
-Entire Microtubules co-polymerised with doublecortin and bound with kine...
|Entire||Name: Microtubules co-polymerised with doublecortin and bound with kinesin motor domain|
Number of components: 3 / Oligomeric State: 13-protofilament microtubule
-Component #1: protein, Alpha-beta tubulin dimer
|Protein||Name: Alpha-beta tubulin dimer / a.k.a: Tubulin dimer / Oligomeric Details: Heterodimer / Recombinant expression: No|
|Source||Species: Bos taurus / mammal / Bovine / Cattle (Wikipedia) /|
|Source (natural)||Location in cell: Cytoplasm / Organ or tissue: Brain|
-Component #2: protein, Doublecortin
|Protein||Name: Doublecortin / a.k.a: DCX / Oligomeric Details: Monomer / Recombinant expression: Yes|
|Source||Species: Homo sapiens / human / Wikipedia|
|Source (engineered)||Expression System: Spodoptera frugiperda / arthropod / Fall armyworm (Wikipedia)|
|Source (natural)||Location in cell: Cytoplasm|
-Component #3: protein, Kinesin motor domain
|Protein||Name: Kinesin motor domain / a.k.a: Kinesin head / Oligomeric Details: Monomer / Recombinant expression: Yes|
|Source||Species: Rattus norvegicus / mammal / Rat / Brown rat (Wikipedia) /|
|Source (engineered)||Expression System: Escherichia coli / bacteria / Wikipedia /|
|Source (natural)||Location in cell: Cytoplasm|
|Sample solution||Buffer solution: 80mM Pipes, 1mM EGTA, 3mM MgCl2, 1mM TCEP, 0.5mM GTP|
|Support film||300 mesh lacey carbon grids|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: Chamber at 37 degrees C, blot 2s / Details: Vitrification instrument: Vitrobot (FEI)|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal)|
Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 760 - 2900 nm
|Specimen Holder||Holder: Eucentric / Model: OTHER / Temperature: 93 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 63 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / Details: Images were binned with a factor of 2|
|Processing||Method: single particle reconstruction|
|3D reconstruction||Algorithm: Custom scripts, projection matching / Software: SPIDER, FREALIGN / CTF correction: FREALIGN|
Details: C1 map calculated from approximately 13,000 one-dimer-long microtubule segments
Resolution: 13.5 Å / Resolution method: FSC 0.5
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi