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Title:Subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase
Authors:Rivera-Calzada A, Fronzes R, Savva CG, Chandran V, Lian PW, Laeremans T, Pardon E, Steyaert J, Remaut H, Waksman G, Orlova EV
Sample:traN/traO/traF complex encoded by pKM101 digested with 0.02 mg ml-1 of elastase for 40 min at room temperature
Method:Single particle reconstruction (8.5 angstroms resolution)
Related entries in frame:EMD-2232
Red flagLatest update:2013-04-24
Sample
Sample name: traN/traO/traF complex encoded by pKM101 digested with 0.02 mg ml-1 of elastase for 40 min at room temperature
Oligomeric state: 14-mer
Theoretical molecular weight of the sample: 0.830
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1proteintraF14-mertrueEscherichia coliIPR005498
2proteintraO14-mertrueEscherichia coliIPR010258
3proteintraN14-mertrueEscherichia coli
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
80.01 mg/mL50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAOcontinuous carbon-coated grids
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE100%92 KFEI VITROBOT MARK IIIblot 4 seconds before plunging ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TECNAI 12200 kVFLOOD BEAMBRIGHT FIELD2.1 mm1500 nm3500 nm6600068100FIELD EMISSION GUNGENERIC GATAN mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Side entry liquid nitrogen-cooled cryo specimen holderGATAN LIQUID NITROGEN°° eV95 K K K mrad20 e/Å24000x4000 CCD11-JAN-2012
Processing
Protocol:common lines
Software:imagic
CTF correction:phase flipping, each CCD image
Number of particles:5430
Number of class averages:1810
Imposed symmetry:C14
Resolution by author:8.5 Å
Resolution method:FSC 0.5
Processing details:Final map was calculated from 5430 particles. Particles picked with BOXER (EMAN).
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
26215 μm/pixel8
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
3JQO flexibleCorrelationChimera, Situs, Sculptor, Flex-EMREALProtocol: Rigid body followed by flexible fitting