2022-04-27 REL PDBe PDBe PDBe 2021-01-12 2022-03-09 2022-03-09 2022-04-27 Cryo-EM structure of the Phosphatidylinositol 3-kinase type 2a (PI3KC2a) of the class II PI3K family Lo WT Zhang Y Vadas O Belabed H Roeske Y Gulluni F De Santis MC Vujicic Zagar A Stephanowitz H Hirsch E Liu F Daumke O Nazare M Kudryashev M Haucke V Lo WT Zhang Y Vadas O Roske Y Gulluni F De Santis MC Zagar AV Stephanowitz H Hirsch E Liu F Daumke O Kudryashev M Haucke V Structural basis of phosphatidylinositol 3-kinase C2 alpha function. Nat.Struct.Mol.Biol. US 29 218 228 2022 35256802 doi:10.1038/s41594-022-00730-w 1545-9985 EMD-12191 associated EM volume Class II PI3KA Class II PI3KA 0 Mus musculus Spodoptera frugiperda 0.15 singleParticle particle 0.8 7.4 20.0 Tris-HCl Tris(hydroxymethyl)aminomethane hydrochloride 100.0 NaCl Sodium chloride
The buffer containing 20 mM Tris-HCl, 100 mM NaCl at pH 7.4.
 Quantifoil GOLD 300 PLASMA CLEANING OTHER
QUANTIFOIL Holey Au-carbon-R2/2 specimen grids were used.
 ETHANE 100 283 FEI VITROBOT MARK IV
The sample was vitrified by plunge-freezing into liquid ethane using a Mark IV Vitrobot device (Thermo Fisher Scientific), blotting force 20, blotting time 4.5-5.5s..
The purified sample was diluted to 0.8 mg/ml into buffer containing 20 mM Tris-HCl, 100 mM NaCl at pH 7.4.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 1.2 2.8000000000000003 3.3000000000000003 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 79.8 89.9 no no 20
Grids were screened first to check ice thickness and particle distribution.
GATAN K3 (6k x 4k) COUNTING 5760 4096 2 10433 3.0 60.0
Images were collected with 50 frames over 60 electrons per squared angstrom.
 1
The images were collected and processed with cryosparc.
2752000
Particles were auto picked with blob picker.
 cryoSPARC V2.12 Patch CTF estimation
CTF estimation was performed after motion correction. And Ctf local refine was performed after 3D reconstruction, in cryosparc.
Ab-initio reconstruction from 2D selected particles
 C1 BACK PROJECTION 4.4 FSC 0.143 CUT-OFF cryoSPARC V2.12 Homogenous refinement 601000 NOT APPLICABLE MAXIMUM LIKELIHOOD cryoSPARC V2.12
stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms
 100 8490.0 cryoSPARC v2.12 2D classification emd_12191.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 217.62001 217.62001 217.62001 90.0 90.0 90.0 X Y Z -0.09764164 0.23457181 0.00014710799 0.009579717 0.837 0.837 0.837 0.05 AUTHOR cryosparc refined map emd_12191_msk_1.map emd_12191_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 217.62001 217.62001 217.62001 90.0 90.0 90.0 X Y Z -0.26274332 0.3984308 0.0003096538 0.01691437 0.837 0.837 0.837 AUTHOR RELION postprocess map emd_12191_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 217.62001 217.62001 217.62001 90.0 90.0 90.0 X Y Z -0.2640706 0.33356977 0.00035690863 0.03648564 0.837 0.837 0.837 AUTHOR half map 2 emd_12191_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 217.62001 217.62001 217.62001 90.0 90.0 90.0 X Y Z -0.2897926 0.32934633 0.0003612601 0.03648575 0.837 0.837 0.837 AUTHOR half map 1