top_cornerHomeEMD-1107  Contact us 
Image unavailable
Title:Structural basis of pore formation by the bacterial toxin pneumolysin.
Authors:Tilley SJ, Orlova EV, Gilbert RJ, Andrew PW, Saibil HR
Sample:Pneumolysin
Aggregation state:Single particle (29 angstroms resolution)
Red flagLatest update:2011-05-26
inner_corner
tab_top_blue.gif
bullet_white.gif  Summary
tab_bottom_blue.gif
pixel.gif
tab_top_white.gif
bullet.png Experimental details
tab_bottom_white.gif
pixel.gif
tab_top_blue.gif
bullet_white.gif  Visualization
tab_bottom_blue.gif
pixel.gif
tab_top_blue.gif
bullet_white.gif  Map information
tab_bottom_blue.gif
pixel.gif
tab_top_blue.gif
bullet_white.gif  Downloads
tab_bottom_blue.gif
pixel.gif
Sample
Sample name: Pneumolysin
Oligomeric state: 38-mer
Theoretical molecular weight of the sample: 2.0
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Mutant Organism GO identifier InterPro identifier Virus identifier Details
1proteinPneumolysin2.038-merfalseStreptococcus pneumoniaeIPR001869
2cellular-componentPhosphatidylcholine-cholesterol lipid bilayerfalsen/a
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
6.950.05 mg/mL8 mM Na2HPO4, 1.5 mM KH2PO4, 2.5 mM KCl, 0.25M NaClholey carbon 400 mesh copper grid, glow discharged using positive charge
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE96%100 Khome made plungerGrids were blotted for approximately 3 seconds and allowed to drain vertically for 5 seconds before plunging. ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TECNAI F20200 kVFLOOD BEAMBRIGHT FIELD2.0 mm1100 nm3200 nm42000FIELD EMISSION GUNKodak SO163 film mmcorrected at 150,000 magnification

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Side entryGATAN LIQUID NITROGEN°° eV100 K100 K100 K mrad20 e/Å2
Processing
Software:Imagic
CTF correction:phase flipping
Resolution by author:29 Å
Resolution method:FSC at 0.5 cut-off
Processing details:Weighted back projection and amplitude scaling were used.
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
1357 μm/pixel18linkAfter scanning images were averaged 2x2.ZEISS SCAI
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
1PFO The 1pfo structure was separated into six rigid bodies: domain 1 (91-172, 231-272, 354-373), domain 2 upper (53-62, 83-90, 374-381), domain 2 lower (63-82, 382-390), domain 3 (177-186, 221-230, 273-283, 316-353), domain 3 hairpins (187-220, 284-315), and domain 4 (391-500). These rigid bodies were fitted manually using the software O and pymol.
outer_corner