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- EMDB-40167: Locally refined cryoEM structure of G protein heterotrimer from b... -
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Title | Locally refined cryoEM structure of G protein heterotrimer from beta-2-adrenergic receptor in complex with GTP-bound Gs heterotrimer (transition intermediate #11 of 20) | |||||||||
![]() | Locally refined cryoEM structure of G protein heterotrimer from beta-2-adrenergic receptor in complex with GTP-bound Gs heterotrimer (transition intermediate #11 of 20) | |||||||||
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![]() | GPCR / Adrenergic / Receptor / G protein / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / response to cold / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / Olfactory Signaling Pathway / Activation of the phototransduction cascade / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to amyloid-beta / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Cargo recognition for clathrin-mediated endocytosis / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / positive regulation of cold-induced thermogenesis / phospholipase C-activating G protein-coupled receptor signaling pathway / amyloid-beta binding / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / receptor complex / cell population proliferation / transcription by RNA polymerase II / positive regulation of MAPK cascade / endosome / cell surface receptor signaling pathway / endosome membrane / early endosome / lysosome / Ub-specific processing proteases / apical plasma membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Papasergi-Scott MM / Skiniotis G | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Time-resolved cryo-EM of G-protein activation by a GPCR. Authors: Makaía M Papasergi-Scott / Guillermo Pérez-Hernández / Hossein Batebi / Yang Gao / Gözde Eskici / Alpay B Seven / Ouliana Panova / Daniel Hilger / Marina Casiraghi / Feng He / Luis Maul ...Authors: Makaía M Papasergi-Scott / Guillermo Pérez-Hernández / Hossein Batebi / Yang Gao / Gözde Eskici / Alpay B Seven / Ouliana Panova / Daniel Hilger / Marina Casiraghi / Feng He / Luis Maul / Peter Gmeiner / Brian K Kobilka / Peter W Hildebrand / Georgios Skiniotis / ![]() ![]() ![]() Abstract: G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating guanine nucleotide exchange in the Gα subunit. To visualize this mechanism, we developed a time-resolved cryo-EM ...G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating guanine nucleotide exchange in the Gα subunit. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G-protein complex. By monitoring the transitions of the stimulatory G protein in complex with the β-adrenergic receptor at short sequential time points after GTP addition, we identified the conformational trajectory underlying G-protein activation and functional dissociation from the receptor. Twenty structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of main events driving G-protein activation in response to GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα switch regions and the α5 helix that weaken the G-protein-receptor interface. Molecular dynamics simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP on closure of the α-helical domain against the nucleotide-bound Ras-homology domain correlates with α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signalling events. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 127.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.2 KB 22.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.8 KB | Display | ![]() |
Images | ![]() | 117.6 KB | ||
Masks | ![]() | 134.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 67.4 MB 124.9 MB 124.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gdzC ![]() 8ge1C ![]() 8ge2C ![]() 8ge3C ![]() 8ge4C ![]() 8ge5C ![]() 8ge6C ![]() 8ge7C ![]() 8ge8C ![]() 8ge9C ![]() 8geaC ![]() 8gebC ![]() 8gecC ![]() 8gedC ![]() 8geeC ![]() 8gefC ![]() 8gegC ![]() 8gehC ![]() 8geiC ![]() 8gejC ![]() 8gfvC ![]() 8gfwC ![]() 8gfxC ![]() 8gfyC ![]() 8gfzC ![]() 8gg0C ![]() 8gg1C ![]() 8gg2C ![]() 8gg3C ![]() 8gg4C ![]() 8gg5C ![]() 8gg6C ![]() 8gg7C ![]() 8gg8C ![]() 8gg9C ![]() 8ggaC ![]() 8ggbC ![]() 8ggcC ![]() 8ggeC ![]() 8ggfC ![]() 8ggiC ![]() 8ggjC ![]() 8ggkC ![]() 8gglC ![]() 8ggmC ![]() 8ggnC ![]() 8ggoC ![]() 8ggpC ![]() 8ggqC ![]() 8ggrC ![]() 8ggsC ![]() 8ggtC ![]() 8gguC ![]() 8ggvC ![]() 8ggwC ![]() 8ggxC ![]() 8ggyC ![]() 8ggzC ![]() 8gh0C ![]() 8gh1C ![]() 8unlC ![]() 8unmC ![]() 8unnC ![]() 8unoC ![]() 8unpC ![]() 8unqC ![]() 8unrC ![]() 8unsC ![]() 8untC ![]() 8unuC ![]() 8unvC ![]() 8unwC ![]() 8unxC ![]() 8unyC ![]() 8unzC ![]() 8uo0C ![]() 8uo1C ![]() 8uo2C ![]() 8uo3C ![]() 8uo4C C: citing same article ( |
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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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Annotation | Locally refined cryoEM structure of G protein heterotrimer from beta-2-adrenergic receptor in complex with GTP-bound Gs heterotrimer (transition intermediate #11 of 20) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8677 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Additional Map
File | emd_40167_additional_1.map | ||||||||||||
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Annotation | Additional Map | ||||||||||||
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-Half map: Half Map 1
File | emd_40167_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
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-Half map: Half Map 2
File | emd_40167_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Complex of beta-2 adrenergic receptor and Gs heterotrimer with GTP
Entire | Name: Complex of beta-2 adrenergic receptor and Gs heterotrimer with GTP |
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Components |
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-Supramolecule #1: Complex of beta-2 adrenergic receptor and Gs heterotrimer with GTP
Supramolecule | Name: Complex of beta-2 adrenergic receptor and Gs heterotrimer with GTP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Combined datasets of the protein complex from samples plunge frozen at 5 sec, 10 sec, or 17 sec after GTP addition to the sample. |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: G protein alpha s (short)
Macromolecule | Name: G protein alpha s (short) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG DSEKATKVQD IKNNLKEAIE TIVAAMSNLV PPVELANPEN QFRVDYILSV MNVPDFDFPP EFYEHAKALW EDEGVRACYE RSNEYQLIDC AQYFLDKIDV ...String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG DSEKATKVQD IKNNLKEAIE TIVAAMSNLV PPVELANPEN QFRVDYILSV MNVPDFDFPP EFYEHAKALW EDEGVRACYE RSNEYQLIDC AQYFLDKIDV IKQADYVPSD QDLLRCRVLT SGIFETKFQV DKVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVASSSYN MVIREDNQTN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG KSKIEDYFPE FARYTTPEDA TPEPGEDPRV TRAKYFIRDE FLRISTASGD GRHYCYPHFT CAVDTENIRR VFNDCRDIIQ RMHLRQYELL UniProtKB: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
-Macromolecule #2: G protein beta 1
Macromolecule | Name: G protein beta 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: GSSGSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK TREGNVRVSR ELAGHTGYLS CCRFLDDNQI VTSSGDTTCA ...String: GSSGSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK TREGNVRVSR ELAGHTGYLS CCRFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DINAICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGVTDDGMAV ATGSWDSFLK IWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #3: G protein gamma 2
Macromolecule | Name: G protein gamma 2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #4: Beta-2 adrenergic receptor
Macromolecule | Name: Beta-2 adrenergic receptor / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGTQQRD EVWVVGMGIV MSLIVLAIVF GNVLVITAIA KFERLQTVTN YFITSLACAD LVMGLAVVPF GAAHILTKTW TFGNFWCEFW TSIDVLCVTA SIETLCVIAV DRYFAITSPF ...String: MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGTQQRD EVWVVGMGIV MSLIVLAIVF GNVLVITAIA KFERLQTVTN YFITSLACAD LVMGLAVVPF GAAHILTKTW TFGNFWCEFW TSIDVLCVTA SIETLCVIAV DRYFAITSPF KYQSLLTKNK ARVIILMVWI VSGLTSFLPI QMHWYRATHQ EAINCYAEET CCDFFTNQAY AIASSIVSFY VPLVIMVFVY SRVFQEAKRQ LQKIDKSEGR FHVQNLSQVE QDGRTGHGLR RSSKFCLKEH KALKTLGIIM GTFTLCWLPF FIVNIVHVIQ DNLIRKEVYI LLNWIGYVNS GFNPLIYCRS PDFRIAFQEL LCLRRSSLKA YGNGYSSNGN TGEQSGLEVL FQGPYHVEQE KENKLLAEDL PGTEDFVGHQ GTVPSDNIDS QGRNASTNDS LLETSQVAPA UniProtKB: Beta-2 adrenergic receptor |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: GTP was added just prior to freezing at 5 sec, 10 sec, or 17 sec before plunging. |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Details: GTP was added just prior to freezing at 5 sec, 10 sec, or 17 sec before plunging.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 Details: The map is the result of combining multiple datasets: cryo-EM imaging of the beta-2AR-Gs + GTP (5 sec) complex was performed on a Titan Krios electron microscope equipped with a K3 Summit ...Details: The map is the result of combining multiple datasets: cryo-EM imaging of the beta-2AR-Gs + GTP (5 sec) complex was performed on a Titan Krios electron microscope equipped with a K3 Summit direct electron detector (Gatan). The microscope was operated at 300 kV accelerating voltage, with a nominal magnification of 105,000x in counting mode resulting in a magnified pixel size of 0.8677 Angstrom. A total exposure of 60.48 electrons/ Angstrom^2 over 63 frames with defocus ranging from -1.0 - -2.0 micrometers was used. Cryo-EM imaging of beta-2AR-Gs + GTP (10 sec) complex was performed on four separate grids over three collection sessions. The microscope was operated at 300 kV accelerating voltage, with a magnification at the camera of 58,679x in counting mode resulting in a magnified pixel size of 0.8521 Angstrom. For the first and second grids, movies were obtained at an exposure rate of 21.13 electrons/Angstrum^2/sec with defocus ranging from -0.4 - -2.0 micrometers. The total exposure time was 2.717 sec over 77 frames per movie stack. For an additional collection of the first grid, movies were obtained at an exposure rate of 20.95 electrons/ Angstrum^2/sec with defocus ranging from -0.4 -2.0 micrometers. The total exposure time was 2.717 sec over 77 frames per movie stack. For the third and fourth grids, movies were obtained at an exposure rate of 30.71 electrons/ Angstrum^2/sec with defocus ranging from -0.5 - -1.6 micrometers. The total exposure time was 2.008 sec over 79 frames per movie stack. Cryo-EM imaging of beta-2AR-Gs + GTP (17 sec) was performed on a Titan Krios equipped with a post-column energy filter, with a magnification of 105,000x in counting mode resulting in a magnified pixel size of 0.8677 Angstrom. Movies were obtained at an exposure rate of 32.46 electrons/Angstrum^2/sec with defocus ranging from -0.4 - -0.9 micrometers. The total exposure time was 1.999 sec over 79 frames per movie stack. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |