REL PDBe PDBe PDBe 2005-01-19 2005-01-20 2005-01-20 2012-10-17 Structural basis of pore formation by the bacterial toxin pneumolysin. Tilley SJ Orlova EV Gilbert RJ Andrew PW Saibil HR Tilley SJ Orlova EV Gilbert RJ Andrew PW Saibil HR Structural basis of pore formation by the bacterial toxin pneumolysin. CELL(CAMBRIDGE,MASS.) 121 247 256 2005 15851031 doi:10.1016/j.cell.2005.02.033 2bk1 FULLOVERLAP Pneumolysin Pneumolysin 2 Phosphatidylcholine-cholesterol lipid bilayer false synthetic construct membrane Pneumolysin Streptococcus pneumoniae cytoplasm true Escherichia coli pKK233-2 IPR001869 singleParticle particle 0.05 6.95
8 mM Na2HPO4, 1.5 mM KH2PO4, 2.5 mM KCl, 0.25M NaCl
holey carbon 400 mesh copper grid, glow discharged using positive charge
 ETHANE 96 100 HOMEMADE PLUNGER
Vitrification instrument: home made plunger
Grids were blotted for approximately 3 seconds and allowed to drain vertically for 5 seconds before plunging. FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 1.1 3.2 40000.0 GATAN LIQUID NITROGEN 100 100 100 corrected at 150,000 magnification KODAK SO-163 FILM ZEISS SCAI 7 135 20
After scanning images were averaged 2x2.
1.0 8. Side entry
Prior to vitrification pneumolysin was added to freshly prepared liposomes consisting of 10:10:1 molar ratio of PC: cholestrol: dicetylphosphate. Pneumolysin was added at a molar ratio of 1:2000 for dialysed liposomes or 1:4000 for extruded liposomes and placed on ice for 5 minutes. This mixture was incubated at 37C for 3 minutes before application to the grid.
phase flipping
 OTHER 28.0 FSC 0.5 CUT-OFF Imagic
Weighted back projection and amplitude scaling were used. This map was calculated from the weighted sum of segments of two pneumolysin pore maps of different diameters, one calculated using c38 symmetry and the other calculated using c44 symmetry.
131
Tomographic series around symmetry axis.
 17 emd_1108.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 -80 -80 -80 160 160 160 560 560 560 90 90 90 X Y Z -66.541300000000007 67.437100000000001 -0.00283751 2.52878 3.5 3.5 3.5 2.53 This 3D map is the weighted average of two pneumolysin pore maps of different sizes.
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 1PFO RIGID BODY FIT
The 1pfo structure was separated into six rigid bodies: domain 1 (91-172, 231-272, 354-373), domain 2 upper (53-62, 83-90, 374-382), domain 2 lower (63-82, 382-390), domain 3 (177-186, 221-230, 273-283, 316-355), domain 3 hairpins (187-220, 284-315), and domain 4 (391-500). These rigid bodies were fitted manually using the software O and pymol.