Structure of the phosphoinositide 3-kinase p110 gamma (PIK3CG) p101 (PIK3R5) complex

2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATA_COLLECTION chem_comp_atom chem_comp_bond STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name RCSB RCSB 2021-04-08 2021-07-14 2021-07-14 2025-05-14 Canadian Institutes of Health Research (CIHR) 168998 Canada Structure of the phosphoinositide 3-kinase p110 gamma (PIK3CG) p101 (PIK3R5) complex Burke JE Dalwadi U Rathinaswamy MK Yip CK PI3K, p110, PIK3CG, PIK3R5, p101, phosphoinositide 3-kinase, PIP3, IMMUNE SYSTEM, TRANSFERASE Rathinaswamy MK Dalwadi U Fleming KD Adams C Stariha JTB Pardon E Baek M Vadas O DiMaio F Steyaert J Hansen SD Yip CK Burke JE Structure of the phosphoinositide 3-kinase (PI3K) p110 gamma-p101 complex reveals molecular mechanism of GPCR activation. Sci Adv US 7 2021 34452907 doi:10.1126/sciadv.abj4282 2375-2548 7mez FULLOVERLAP Ternary complex of p110 gamma with p101 and a p101 binding nanobody Ternary complex of p110 gamma with p101 and a p101 binding nanobody 0 1 2

Nanobody binds to GBD domain, but was too fleixble to be built in the atomic model

Homo sapiens Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform Homo sapiens 0.126627406 1 Spodoptera frugiperda LEVO MELENYKQPVVLREDNCRRRRRMKPRSAAASLSSMELIPIEFVLPTSQRKCKSPETALLHVAGHGNVEQMKAQVWLRALE TSVAADFYHRLGPHHFLLLYQKKGQWYEIYDKYQVVQTLDCLRYWKATHRSPGQIHLVQRHPPSEESQAFQRQLTALIGY DVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDT PGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRK EEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTS PKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEY VLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIA TDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENV RAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAY LRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEK CKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIE IVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNL FHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMP QLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSA P48736 2.7.1.137 Phosphoinositide 3-kinase regulatory subunit 5 Sus scrofa 0.097471805 1 Spodoptera frugiperda LEVO GAGTMQPGATTCTEDRIQHALERCLHGLSLSRRSTSWSAGLCLNCWSLQELVSRDPGHFLILLEQILQKTREVQEKGTYD LLAPLALLFYSTVLCTPHFPPDSDLLLKAARTYHRFLTWPVPYCSICQELLTFIDAELKAPGISYQRLVRAEQGLSTRSH RSSTVTVLLLNPVEVQAEFLDVADKLSTPGPSPHSAYITLLLHAFQATFGAHCDLSGLHRRLQSKTLAELEAIFTETAEA QELASGIGDAAEARQWLRTKLQAVGEKAGFPGVLDTAKPGKLRTIPIPVARCYTYSWNQDSFDILQEILLKEQELLQPEI LDDEEDEDEEDEEEDLDADGHCAERDSVLSTGSAASHASTLSLASSQASGPTLSRQLLTSFVSGLSDGVDSGYMEDIEES AYERPRRPGGHERRGHRRPGQKFNRIYKLFKSTSQMVLRRDSRSLEGSPDSGPPLRRAGSLCSPLDSPTLPPSRAQRSRS LPQPKLSPQLPGWLLAPASRHQRRRPFLSGDEDPKASTLRVVVFGSDRISGKVARAYSNLRRLENNRPLLTRFFKLQFFY VPVKRSRGTGTPTSPAPRSQTPPLPTDAPRHPGPAELGAAPWEESTNDISHYLGMLDPWYERNVLGLMHLPPEVLCQSLK AEPRPLEGSPAQLPILADMLLYYCRFAARPVLLQVYQTELTFITGEKTTEIFIHSLELGHSAATRAIKASGPGSKRLGID GDREAVPLTLQIIYSKGAISGRSRWSNMEKLCTSVNLSKACRQQEELDSSTEALTLNLTEVVKRQTPKSKKGFNQISTSQ IKVDKVQIIGSNSCPFAVCLDQDERKILQSVIRCEVSPCYKPEKSSLCPPPQRPSYPPAPATPDLCSLLCLPIMTFSGAL P O02696 singleParticle particle 0.45 8.5 20.0 TrisHCl Tris(hydroxymethyl)aminomethane-Hydrochloric acid 100.0 NaCl Sodium Chloride 50.0 (NH4)2SO4 Ammonium Sulfate 0.5 TCEP Tris(2-carboxyethyl)phosphine

Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed

C-flat-2/2 COPPER 300 GLOW DISCHARGE 25 AIR 0.039

Glow discharged using the Pelco EasiGlow. 15mA Current.

ETHANE 100 277 FEI VITROBOT MARK IV

1.5s blot time, -5 blot force.

Specimen was a 1:1:1 molar ratio of p110g-p101-nanobody, purified to homogeneity by gel filtration.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.4 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 6808 36.4

Movies were collected in super-resolution mode set to collect 3 shots per grid hole over 9 holes by beam-shift before applying a stage shift.

All data processing carried out using cryoSPARC v2.18 or newer. Movies were subjected to patch motion correction and 2x2 binning. CTFs of the resulting micrographs were estimated using patch CTF estimation. Template picking using 2D averages low-pass filtered to 20A was carried out before 1 round of 2D and 1 round of 3D classification. Best particles were refined by local motion correction, then subjected to 1 more round of 3D classification. Best class/particles were refined by homogeneous refinement, followed by CTF/defocus refinement and a final non-uniform refinement step.

3762631

Particles were picked using the cryoSPARC template picker

cryoSPARC 3.0 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio reconstruction with 2 classes

1 C1 2.89 FSC 0.143 CUT-OFF cryoSPARC 3.0

cryoSPARC local refinement job (L) from v3.0

320179 MAXIMUM LIKELIHOOD cryoSPARC 3.0

cryoSPARC SGD-based ab intio reconstruction

MAXIMUM LIKELIHOOD cryoSPARC 3.0

cryoSPARC non-uniform refinement

emd_23808.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 317.7 317.7 317.7 90.0 90.0 90.0 X Y Z -3.5281403 7.714876 -0.002197762 0.1345252 1.059 1.059 1.059 1.2 AUTHOR ::::EMDATABANK.org::::EMD-23808::::