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Yorodumi- EMDB-40655: Phosphoinositide phosphate 3 kinase gamma bound with ADP and two ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40655 | |||||||||
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Title | Phosphoinositide phosphate 3 kinase gamma bound with ADP and two Gbetagamma subunits in State 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Phosphoinositide 3-Kinase / Chemotaxis / Cancer / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / 1-phosphatidylinositol-4-phosphate 3-kinase activity / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / phosphatidylinositol-4,5-bisphosphate 3-kinase / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / 1-phosphatidylinositol-3-kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / phosphatidylinositol-mediated signaling / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / cell migration / G protein-coupled receptor signaling pathway / GTPase activity / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Chen C-L / Tesmer JJG / Bandekar SJ / Cash J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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 | emd_40655.map.gz | 113.4 MB | EMDB map data format | |
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Header (meta data) | emd-40655-v30.xml emd-40655.xml | 27 KB 27 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40655_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_40655.png | 122.5 KB | ||
Filedesc metadata | emd-40655.cif.gz | 8.4 KB | ||
Others | emd_40655_half_map_1.map.gz emd_40655_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40655 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40655 | HTTPS FTP |
-Related structure data
Related structure data | 8soeMC 8so9C 8soaC 8sobC 8socC 8sodC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40655.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_40655_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40655_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2
Entire | Name: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2 |
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Components |
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-Supramolecule #1: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2
Supramolecule | Name: PI3K-gamma-ADP bound with two Gbetagamma subunits in State 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 210 kDa/nm |
-Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 37.41693 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #2: phosphatidylinositol-4,5-bisphosphate 3-kinase
Macromolecule | Name: phosphatidylinositol-4,5-bisphosphate 3-kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 127.573531 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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 #3: Phosphoinositide 3-kinase regulatory subunit 5
Macromolecule | Name: Phosphoinositide 3-kinase regulatory subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 98.497773 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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 |
-Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 8.673959 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HHHHHHMASN NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFREK KFFSAIL UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 / Support film - Material: GOLD / Support film - topology: HOLEY | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 2. |
-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: FIELD EMISSION GUN |
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 |
+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-8soe: |