|Entry||Database: EMDB / ID: 2077|
|Title||Electron cryo-microscopy of microtubule-bound human kinesin-5 motor domain in AMPPNP state.|
|Keywords||cancer / electron cryo-microscopy / kinesin / microtubule / mitosis|
|Sample||13-protofilament microtubule-bound human kinesin-5 motor domain with AMPPNP|
|Source||Bos taurus / mammal / Cattle / ウシ / |
Homo sapiens / human
|Map data||3D reconstruction of microtubule-bound human kinesin-5 motor domain with AMPPNP bound in the nucleotide-binding site|
|Method||single particle reconstruction, at 9.7 Å resolution|
|Authors||Goulet A / Behnke-Parks WM / Sindelar C / Rosenfeld S / Moores C|
|Citation||J. Biol. Chem., 2012, 287, 44654-44666|
|Validation Report||PDB-ID: 4aqv|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 19, 2012 / Header (metadata) release: May 17, 2012 / Map release: Nov 21, 2012 / Last update: Jan 9, 2013|
Downloads & links
|File||emd_2077.map.gz (map file in CCP4 format, 357 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.8 Å|
CCP4 map header:
-Entire 13-protofilament microtubule-bound human kinesin-5 motor domain w...
|Entire||Name: 13-protofilament microtubule-bound human kinesin-5 motor domain with AMPPNP|
Number of components: 2
Oligomeric State: 13-protofilament microtubule with one kineisn-5 motor domain bound every tubulin heterodimers
-Component #1: protein, alpha-beta tubulin dimer
|Protein||Name: alpha-beta tubulin dimer / Oligomeric Details: heterodimer / Recombinant expression: No|
|Source||Species: Bos taurus / mammal / Cattle / ウシ /|
|Source (natural)||Organ or tissue: brain|
-Component #2: protein, Kinesin-5 motor domain
|Sample solution||Buffer solution: 80 mM PIPES, 5 mM MgCl2, 1 mM EGTA, 5mM AMPPNP|
|Support film||400 mesh holey carbon grids|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Method: chamber at 24 degrees C, blot 2.5 sec|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Jan 10, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 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: 700 - 2200 nm
|Specimen Holder||Model: GATAN LIQUID NITROGEN / Temperature: 90 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 46 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8|
|Processing||Method: single particle reconstruction / Number of projections: 3587|
Details: The particles were selected along individual microtubules.
|3D reconstruction||Software: SPIDER, FREALIGN / CTF correction: FREALIGN|
Details: Approximately 50,000 asymmetric units were averaged in the final reconstruction.
Resolution: 9.7 Å / Resolution method: FSC 0.5
-Atomic model buiding
|Modeling #1||Software: Chimera, FlexEM / Refinement protocol: flexible / Target criteria: cross-correlation / Refinement space: REAL|
Details: Protocol: rigid body then flexible fitting. The domain was fitted as a rigid body. The N-terminal residues 6 to 16 were built in the EM map and the final model was refined by flexible fitting.
Input PDB model: 3HQD
Chain ID: A
|Modeling #2||Software: Chimera / Refinement protocol: rigid body / Target criteria: cross-correlation / Refinement space: REAL|
Details: Protocol: rigid body. alpha- and b-tubulin were separately fitted.
Input PDB model: 1JFF
Chain ID: A, B
-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
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