2024-05-15 REL PDBe RCSB PDBe 2016-01-05 2016-03-09 2016-04-06 2024-05-15 Medical Research Council (United Kingdom) MC-A021-53019 United Kingdom Wellcome Trust WT089618MA United Kingdom Cryo-EM structure of the Lysenin Pore Savva CG Bokori-Brown M Pore forming protein, aerolysin, toxin Bokori-Brown M Martin TG Naylor CE Basak AK Titball RW Savva CG Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein Nat Commun UK 7 11293 11293 2016 27048994 doi:10.1038/ncomms11293 2041-1723 5gaq FULLOVERLAP Membrane-inserted form of the nonameric pore forming protein Lysenin Membrane-inserted form of the nonameric pore forming protein Lysenin 0 1 Eisenia foetida 0.315 Lysenin Eisenia fetida 0.034977246 9 Escherichia coli LEVO MSAKAAEGYEQIEVDVVAVWKEGYVYENRGSTSVDQKITITKGMKNVNSETRTVTATHSIGSTISTGDAFEIGSVEVSYS HSHEESQVSMTETEVYESKVIEHTITIPPTSKFTRWQLNADVGGADIEYMYLIDEVTPIGGTQSIPQVITSRAKIIVGRQ IILGKTEIRIKHAERKEYMTVVSRKSWPAATLGHSKLFKFVLYEDWGGFRIKTLNTMYSGYEYAYSSDQGGIYFDQGTDN PKQRWAINKSLPLRHGDVVTFMNKYFTRSGLCYDDGPATNVYCLDKREDKWILEVVGLVPRGSGHHHHHH O18423 singleParticle particle 0.2 7.4 150.0 Sodium Chloride 50.0 Tris 500.0 Imidazole 0.02 Dodecyl Maltoside Quantifoil R1.2/1.3 GOLD 300 GRAPHENE CONTINUOUS
Grids were glow-discharged prior to deposition of Graphene-oxide.No further treatment was performed after graphene-oxide deposition.
 ETHANE 90 277 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 0.7000000000000001 4.5 4.7 81000.0 34965.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 85.0 85.0 GIF Quantum 0 20
Direct alignments: Beam tilt pivot points, Beam shift, Comma Free. C2 aperture centering, C2 lens astigmatism correction. Objective aperture centering and objective lens astigmatism correction. Energy filter Tuning and occasional ZLP centering.
GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3710 3710 0-20 1 280 18.0 47.0 1
Super-resolution images were binned by 2 for further processing.
53779
Autopicking performed with RELION after manually picking 1000 particles to create 2D Classes (references) for autopicking.
Using EMAN 2 makeinitialmodel
 C9 3.1 FSC 0.143 CUT-OFF RELION 1.4 29329 PROJECTION MATCHING 7.5 RELION 1.4 PROJECTION MATCHING 0.47 RELION 1.4 3 15000.0 RELION 1.4
3D classification was used to reduced particle heterogeneity in final reconstruction
 emd_8015.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 320.31998 320.31998 320.31998 90.0 90.0 90.0 X Y Z -0.17919779 0.3905925 0.0005988714 0.009276755 1.43 1.43 1.43 0.07 AUTHOR None 3ZXD A 150-297 PDB experimental model AB INITIO MODEL
Initial docking of C-terminal region of lysenin monomer to EM map was performed using UCSF Chimera followed by model N-terminal extension in COOT.
REAL