top_cornerHomeEMD-5896  Contact EMDataBank 
Image unavailable
Title:Cryo EM density of GDP-bound dynamic microtubules
Authors:Alushin GM, Lander GC, Kellogg EH, Zhang R, Baker D, Nogales E
Sample:Dynamic GDP-bound microtubule
Method:Single particle reconstruction (4.9 angstroms resolution)
Sample
Sample name: Dynamic GDP-bound microtubule
Components:
ID Type Name Exp. MW (MDa) Theo. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1proteinAlpha tubulin0.055heterodimerfalseSus scrofa
2proteinBeta tubulin0.055heterodimerfalseSus scrofa
3proteinkinesin0.036monomertrueHomo sapiensHuman monomeric kinesin K349 cys-lite described in: Rice, S., Lin, A.W., Safer, D., Hart, C.L., Naber, N., Carragher, B.O., Cain, S.M., Pechatnikova, E., Wilson-Kubalek, E.M., Whittaker, M., et al. (1999). A structural change in the kinesin motor protein that drives motility. Nature 402, 778-784.
Experiment
Specimen state: Helical array
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
6.80.25 mg/mL80mM PIPES, 1mM EGTA, 1mM MgCl2, 1mM DTT, 0.05% Nonidet P-40400 mesh C-flat 1.2/1.3, glow discharged in Edwards carbon evaporator
Helical parameters:
HandPhi incrementAzimuthal (Z) incrementRotational symmetry
LEFT HANDED25.76°8.82 ÅC1
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE90%90.4 KFEI VITROBOT MARK IIThe grid was blotted for 2 seconds before plunging. ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TITAN300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1400 nm3500 nm7200072000FIELD EMISSION GUNKODAK SO-163 FILM mmObjective lens astigmatism was corrected at 100,000 times magnifacation.

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Gatan 626 holderGATAN LIQUID NITROGEN eV K K K mrad25.0 e/Å215-JUN-2012
Processing
Protocol:projection matching
Software:FREALIGN
CTF correction:ctftilt
Number of particles:54445
Imposed symmetry:C1
Resolution by author:4.9 Å
Resolution method:FSC 0.143, semi-independent
Processing details:Initial alignments performed with EMAN2/SPARX, including refinement of helical parameters with the IHRSR programs of Egelman. Final alignment and reconstruction performed with FREALIGN.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
2196.35 μm/pixel16NIKON SUPER COOLSCAN 8000
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
1JFF flexibleROSETTAREALStructure represents the minimized average structure of the 1% lowest energy structures from the refinement run.