2024-05-01 REL PDBe PDBe PDBe 2020-06-13 2020-11-18 2020-11-18 2024-05-01 Cancer Research UK C26409/A16099 United Kingdom Disulfide-locked early prepore intermedilysin-CD59 Shah NR Bubeck D early prepore, membrane-bound, oligomer, TOXIN Shah NR Voisin TB Parsons ES Boyd CM Hoogenboom BW Bubeck D Structural basis for tuning activity and membrane specificity of bacterial cytolysins. Nat Commun UK 11 5818 5818 2020 33199689 doi:10.1038/s41467-020-19482-6 2041-1723 6zd0 FULLOVERLAP Early prepore of intermedilysin-CD59 Early prepore of intermedilysin-CD59 0 1 2
Prepore is formed on a lipid bilayer on a nanodisc
 Thiol-activated cytolysin 1 1 Streptococcus intermedius CD59 glycoprotein 1 2 Homo sapiens Thiol-activated cytolysin Streptococcus intermedius 0.059100953 3 Escherichia coli BL21(DE3) LEVO MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSETPTKPKAAQTEKKTEKKPENSNSEAAKKALNDYIWGLQYDKLN ILTHQGEKLKNHSSREAFHRPGEYVVCEKKKQSISNATSKLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTI SVNLPGLKNGESNLTVENPSNSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVD FSSVHKCEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNVSYGRAMYVKFETTSKSTKV QAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEASKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDN SIATIQNNTDYIETKVTSYKDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVR NIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVKDNTD Q9LCB8 CD59 glycoprotein Homo sapiens 0.009204444999999999 3 Escherichia coli LEVO MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENELTYYCCKKDLCNFNEQLENC P13987 singleParticle particle 7.5 20.0 (HOCH2)3CNH2 Tris 200.0 NaCl sodium chloride Quantifoil R1.2/1.3 COPPER 400 GRAPHENE OXIDE CONTINUOUS GLOW DISCHARGE AIR
Grids were glow discharged before application of graphene oxide, then left to dry for 1 hour before use.
 ETHANE 95 294 FEI VITROBOT MARK III
Wait time of 60 s, blot time 2.5 s, blot force 3.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.9000000000000001 3.1 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
Pixel size 1.4 A
FEI FALCON III (4k x 4k) INTEGRATING 1.0 66.0
Some images were collected at a 30 degree tilt. Images were collected in movie mode at 39 frames per second.
 1 A previous data set was used to generate a 8.6 A reconstruction, which was used as the startup model. 2 4.6 FSC 0.143 CUT-OFF RELION 51041 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION 4 RELION emd_11172.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 210.0 210.0 210.0 90.0 90.0 90.0 X Y Z -0.072169185 0.19049014 0.0015517144 0.013816901 1.4 1.4 1.4 0.022 AUTHOR Half map 1 of ILY-CD59 early prepore oligomer formed on a lipid nanodsic, 5 subunits 4BIK PDB experimental model RIGID BODY FIT
Model of ILY-CD59 was fit and refined into the central subunit density. A combination of rigid body fitting and global minimization with secondary structure restraints was used to fit and refine the central subunit model. Then the central subunit model was rigid body fit as one body into the neighbouring subunits to generate a 3 subunit oligomer model.
REAL emd_11172_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 210.0 210.0 210.0 90.0 90.0 90.0 X Y Z -0.019776957 0.06753876 0.0008911154 0.006258713 1.4 1.4 1.4 AUTHOR Half map 2 of ILY-CD59 early prepore oligomer formed on a lipid nanodsic, 5 subunits emd_11172_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 210.0 210.0 210.0 90.0 90.0 90.0 X Y Z -0.01897816 0.067131266 0.0008927096 0.0062735467 1.4 1.4 1.4 AUTHOR Half map 2 of ILY-CD59 early prepore oligomer formed on a lipid nanodsic, 5 subunits