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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Phosphoinositide phosphate 3 kinase gamma | |||||||||
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![]() | Phosphoinositide 3-Kinase / Chemotaxis / Cancer / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / cell migration / G protein-coupled receptor signaling pathway / ATP binding ...1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / cell migration / G protein-coupled receptor signaling pathway / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
![]() | Chen C-L / Tesmer JJG / Bandekar SJ / Cash J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for Gβγ-mediated activation of phosphoinositide 3-kinase γ. Authors: Chun-Liang Chen / Ramizah Syahirah / Sandeep K Ravala / Yu-Chen Yen / Thomas Klose / Qing Deng / John J G Tesmer / ![]() Abstract: The conversion of phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-triphosphate by phosphoinositide 3-kinase γ (PI3Kγ) is critical for neutrophil chemotaxis and cancer metastasis. ...The conversion of phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-triphosphate by phosphoinositide 3-kinase γ (PI3Kγ) is critical for neutrophil chemotaxis and cancer metastasis. PI3Kγ is activated by Gβγ heterodimers released from G protein-coupled receptors responding to extracellular signals. Here we determined cryo-electron microscopy structures of Sus scrofa PI3Kγ-human Gβγ complexes in the presence of substrates/analogs, revealing two Gβγ binding sites: one on the p110γ helical domain and another on the p101 C-terminal domain. Comparison with PI3Kγ alone reveals conformational changes in the kinase domain upon Gβγ binding that are similar to Ras·GTP-induced changes. Assays of variants perturbing the Gβγ binding sites and interdomain contacts altered by Gβγ binding suggest that Gβγ recruits the enzyme to membranes and allosterically regulates activity via both sites. Studies of zebrafish neutrophil migration align with these findings, paving the way for in-depth investigation of Gβγ-mediated activation mechanisms in this enzyme family and drug development for PI3Kγ. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 114.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23 KB 23 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 91 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8so9MC ![]() 8soaC ![]() 8sobC ![]() 8socC ![]() 8sodC ![]() 8soeC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40650_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40650_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : PI3K-gamma containing the p110gamma catalytic subunit and the p10...
Entire | Name: PI3K-gamma containing the p110gamma catalytic subunit and the p101 regulatory subunit |
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Components |
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-Supramolecule #1: PI3K-gamma containing the p110gamma catalytic subunit and the p10...
Supramolecule | Name: PI3K-gamma containing the p110gamma catalytic subunit and the p101 regulatory subunit type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 210 kDa/nm |
-Macromolecule #1: phosphatidylinositol-4,5-bisphosphate 3-kinase
Macromolecule | Name: phosphatidylinositol-4,5-bisphosphate 3-kinase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 127.573531 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHELE NYEQPVVLRE DNRRRRRRMK PRSTAASLSS MELIPIEFVL PTSQRNTKTP ETALLHVAGH GNVEQMKAQV WLRALETSV SADFYHRLGP DHFLLLYQKK GQWYEIYDKY QVVQTLDCLR YWKVLHRSPG QIHVVQRHAP SEETLAFQRQ L NALIGYDV ...String: MHHHHHHELE NYEQPVVLRE DNRRRRRRMK PRSTAASLSS MELIPIEFVL PTSQRNTKTP ETALLHVAGH GNVEQMKAQV WLRALETSV SADFYHRLGP DHFLLLYQKK GQWYEIYDKY QVVQTLDCLR YWKVLHRSPG QIHVVQRHAP SEETLAFQRQ L NALIGYDV TDVSNVHDDE LEFTRRRLVT PRMAEVAGRD PKLYAMHPWV TSKPLPEYLL KKITNNCVFI VIHRSTTSQT IK VSADDTP GTILQSFFTK MAKKKSLMDI PESQNERDFV LRVCGRDEYL VGETPIKNFQ WVRQCLKNGE EIHLVLDTPP DPA LDEVRK EEWPLVDDCT GVTGYHEQLT IHGKDHESVF TVSLWDCDRK FRVKIRGIDI PVLPRTADLT VFVEANIQYG QQVL CQRRT SPKPFTEEVL WNVWLEFSIK IKDLPKGALL NLQIYCGKAP ALSGKTSAEM PSPESKGKAQ LLYYVNLLLI DHRFL LRHG EYVLHMWQLS GKGEDQGSFN ADKLTSATNP DKENSMSISI LLDNYCHPIA LPKHRPTPDP EGDRVRAEMP NQLRKQ LEA IIATDPLNPL TAEDKELLWH FRYESLKDPK AYPKLFSSVK WGQQEIVAKT YQLLAKREVW DQSALDVGLT MQLLDCN FS DENVRAIAVQ KLESLEDDDV LHYLLQLVQA VKFEPYHDSA LARFLLKRGL RNKRIGHFLF WFLRSEIAQS RHYQQRFA V ILEAYLRGCG TAMLHDFTQQ VQVIDMLQKV TIDIKSLSAE KYDVSSQVIS QLKQKLENLQ NLNLPQSFRV PYDPGLKAG ALVIEKCKVM ASKKKPLWLE FKCADPTALS NETIGIIFKH GDDLRQDMLI LQILRIMESI WETESLDLCL LPYGCISTGD KIGMIEIVK DATTIAKIQQ STVGNTGAFK DEVLSHWLKE KCPIEEKFQA AVERFVYSCA GYCVATFVLG IGDRHNDNIM I SETGNLFH IDFGHILGNY KSFLGINKER VPFVLTPDFL FVMGTSGKKT SLHFQKFQDV CVKAYLALRH HTNLLIILFS MM LMTGMPQ LTSKEDIEYI RDALTVGKSE EDAKKYFLDQ IEVCRDKGWT VQFNWFLHLV LGIKQGEKHS A UniProtKB: phosphatidylinositol-4,5-bisphosphate 3-kinase |
-Macromolecule #2: Phosphoinositide 3-kinase regulatory subunit 5
Macromolecule | Name: Phosphoinositide 3-kinase regulatory subunit 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 98.497773 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MQPGATTCTE DRIQHALERC LHGLSLSRRS TSWSAGLCLN CWSLQELVSR DPGHFLILLE QILQKTREVQ EKGTYDLLAP LALLFYSTV LCTPHFPPDS DLLLKAARTY HRFLTWPVPY CSICQELLTF IDAELKAPGI SYQRLVRAEQ GLSTRSHRSS T VTVLLLNP ...String: MQPGATTCTE DRIQHALERC LHGLSLSRRS TSWSAGLCLN CWSLQELVSR DPGHFLILLE QILQKTREVQ EKGTYDLLAP LALLFYSTV LCTPHFPPDS DLLLKAARTY HRFLTWPVPY CSICQELLTF IDAELKAPGI SYQRLVRAEQ GLSTRSHRSS T VTVLLLNP VEVQAEFLDV ADKLSTPGPS PHSAYITLLL HAFQATFGAH CDLSGLHRRL QSKTLAELEA IFTETAEAQE LA SGIGDAA EARQWLRTKL QAVGEKAGFP GVLDTAKPGK LRTIPIPVAR CYTYSWNQDS FDILQEILLK EQELLQPEIL DDE EDEDEE DEEEDLDADG HCAERDSVLS TGSAASHAST LSLASSQASG PTLSRQLLTS FVSGLSDGVD SGYMEDIEES AYER PRRPG GHERRGHRRP GQKFNRIYKL FKSTSQMVLR RDSRSLEGSP DSGPPLRRAG SLCSPLDSPT LPPSRAQRSR SLPQP KLSP QLPGWLLAPA SRHQRRRPFL SGDEDPKAST LRVVVFGSDR ISGKVARAYS NLRRLENNRP LLTRFFKLQF FYVPVK RSR GTGTPTSPAP RSQTPPLPTD APRHPGPAEL GAAPWEESTN DISHYLGMLD PWYERNVLGL MHLPPEVLCQ SLKAEPR PL EGSPAQLPIL ADMLLYYCRF AARPVLLQVY QTELTFITGE KTTEIFIHSL ELGHSAATRA IKASGPGSKR LGIDGDRE A VPLTLQIIYS KGAISGRSRW SNMEKLCTSV NLSKACRQQE ELDSSTEALT LNLTEVVKRQ TPKSKKGFNQ ISTSQIKVD KVQIIGSNSC PFAVCLDQDE RKILQSVIRC EVSPCYKPEK SSLCPPPQRP SYPPAPATPD LCSLLCLPIM TFSGALPGGG GSDYKDDDD K UniProtKB: Phosphoinositide 3-kinase regulatory subunit 5 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharge with 20 mA for 1 minute | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 2. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 0.01 mrad |
Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Average exposure time: 3.12 sec. / Average electron dose: 55.0 e/Å2 Details: Images were collected in movie-mode at 40 frames per second |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: correlation coefficient | ||||||
Output model | ![]() PDB-8so9: |