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Yorodumi- EMDB-29967: CryoEM structure of beta-2-adrenergic receptor in complex with nu... -
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Basic information
| Entry |  | |||||||||
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| Title | CryoEM structure of beta-2-adrenergic receptor in complex with nucleotide-free Gs heterotrimer (#15 of 20) | |||||||||
|  Map data | Sharpened map | |||||||||
|  Sample | 
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|  Keywords | GPCR / Adrenergic / Receptor / G protein / SIGNALING PROTEIN | |||||||||
| Function / homology |  Function and homology information positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / endosome to lysosome transport / adrenergic receptor signaling pathway / response to psychosocial stress / diet induced thermogenesis / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / bone resorption / D1 dopamine receptor binding / potassium channel regulator activity / positive regulation of bone mineralization / neuronal dense core vesicle / intracellular transport / brown fat cell differentiation / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to glucagon stimulus / regulation of insulin secretion / receptor-mediated endocytosis / response to cold / adenylate cyclase activator activity / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / clathrin-coated endocytic vesicle membrane / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / platelet aggregation / cognition / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition  of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / cellular response to amyloid-beta / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / mitotic spindle / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / sensory perception of smell / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / Cargo recognition for clathrin-mediated endocytosis / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / retina development in camera-type eye / G protein activity / microtubule cytoskeleton / GTPase binding / Ca2+ pathway Similarity search - Function | |||||||||
| Biological species |  Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
|  Authors | Papasergi-Scott MM / Skiniotis G | |||||||||
| Funding support |  United States, 2 items 
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|  Citation |  Journal: Nature / Year: 2024 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
Structure visualization
| Supplemental images | 
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- Downloads & links
Downloads & links
-EMDB archive
| Map data |  emd_29967.map.gz | 97.3 MB |  EMDB map data format | |
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| Header (meta data) |  emd-29967-v30.xml  emd-29967.xml | 22.9 KB 22.9 KB | Display Display |  EMDB header | 
| FSC (resolution estimation) |  emd_29967_fsc.xml | 9.9 KB | Display |  FSC data file | 
| Images |  emd_29967.png | 100.4 KB | ||
| Masks |  emd_29967_msk_1.map | 103 MB |  Mask map | |
| Filedesc metadata |  emd-29967.cif.gz | 7 KB | ||
| Others |  emd_29967_additional_1.map.gz  emd_29967_half_map_1.map.gz  emd_29967_half_map_2.map.gz | 51.6 MB 95.5 MB 95.5 MB | ||
| Archive directory |  http://ftp.pdbj.org/pub/emdb/structures/EMD-29967  ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29967 | HTTPS FTP | 
-Validation report
| Summary document |  emd_29967_validation.pdf.gz | 1.1 MB | Display |  EMDB validaton report | 
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| Full document |  emd_29967_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML |  emd_29967_validation.xml.gz | 18.4 KB | Display | |
| Data in CIF |  emd_29967_validation.cif.gz | 23.7 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29967  ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29967 | HTTPS FTP | 
-Related structure data
| Related structure data |  8geeMC  8gdzC  8ge1C  8ge2C  8ge3C  8ge4C  8ge5C  8ge6C  8ge7C  8ge8C  8ge9C  8geaC  8gebC  8gecC  8gedC  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 M: atomic model generated by this map C: citing same article ( | 
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| Similar structure data | Similarity search - Function & homology  F&H Search | 
- Links
Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
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| Related items in Molecule of the Month | 
- Map
Map
| File |  Download / File: emd_29967.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
 
 Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
| Density | 
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML: 
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-Supplemental data
-Mask #1
| File |  emd_29967_msk_1.map | ||||||||||||
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| Projections & Slices | 
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| Density Histograms | 
-Additional map: Unsharpened map
| File | emd_29967_additional_1.map | ||||||||||||
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| Annotation | Unsharpened map | ||||||||||||
| Projections & Slices | 
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| Density Histograms | 
-Half map: Half map
| File | emd_29967_half_map_1.map | ||||||||||||
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| Annotation | Half map | ||||||||||||
| Projections & Slices | 
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| Density Histograms | 
-Half map: Half map
| File | emd_29967_half_map_2.map | ||||||||||||
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| Annotation | Half map | ||||||||||||
| Projections & Slices | 
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| Density Histograms | 
- Sample components
Sample components
-Entire : Complex of beta-2 adrenergic receptor and Gs heterotrimer
| Entire | Name: Complex of beta-2 adrenergic receptor and Gs heterotrimer | 
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| Components | 
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-Supramolecule #1: Complex of beta-2 adrenergic receptor and Gs heterotrimer
| Supramolecule | Name: Complex of beta-2 adrenergic receptor and Gs heterotrimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 | 
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| Source (natural) | Organism:  Homo sapiens (human) | 
-Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
| Macromolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO | 
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| Source (natural) | Organism:  Homo sapiens (human) | 
| Molecular weight | Theoretical: 44.32616 KDa | 
| Recombinant expression | Organism:  Trichoplusia ni (cabbage looper) | 
| Sequence | String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG DSEKATKVQD  IKNNLKEAI ETIVAAMSNL VPPVELANPE NQFRVDYILS VMNVPDFDFP PEFYEHAKAL WEDEGVRACY ERSNEYQLID C AQYFLDKI  ...String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG DSEKATKVQD  IKNNLKEAI ETIVAAMSNL VPPVELANPE NQFRVDYILS VMNVPDFDFP PEFYEHAKAL WEDEGVRACY ERSNEYQLID C AQYFLDKI DVIKQADYVP SDQDLLRCRV LTSGIFETKF QVDKVNFHMF DVGGQRDERR KWIQCFNDVT AIIFVVASSS YN MVIREDN QTNRLQEALN LFKSIWNNRW LRTISVILFL NKQDLLAEKV LAGKSKIEDY FPEFARYTTP EDATPEPGED PRV TRAKYF IRDEFLRIST ASGDGRHYCY PHFTCAVDTE NIRRVFNDCR DIIQRMHLRQ YELL UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | 
-Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO | 
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| Source (natural) | Organism:  Homo sapiens (human) | 
| Molecular weight | Theoretical: 37.573988 KDa | 
| Recombinant expression | Organism:  Trichoplusia ni (cabbage looper) | 
| Sequence | String: GSSGSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQDG  KLIIWDSYT TNKVHAIPLR SSWVMTCAYA PSGNYVACGG LDNICSIYNL KTREGNVRVS RELAGHTGYL SCCRFLDDNQ I VTSSGDTT  ...String: GSSGSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQDG  KLIIWDSYT TNKVHAIPLR SSWVMTCAYA PSGNYVACGG LDNICSIYNL KTREGNVRVS RELAGHTGYL SCCRFLDDNQ I VTSSGDTT CALWDIETGQ QTTTFTGHTG DVMSLSLAPD TRLFVSGACD ASAKLWDVRE GMCRQTFTGH ESDINAICFF PN GNAFATG SDDATCRLFD LRADQELMTY SHDNIICGIT SVSFSKSGRL LLAGYDDFNC NVWDALKADR AGVLAGHDNR VSC LGVTDD GMAVATGSWD SFLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | 
-Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO | 
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| Source (natural) | Organism:  Homo sapiens (human) | 
| Molecular weight | Theoretical: 7.861143 KDa | 
| Recombinant expression | Organism:  Trichoplusia ni (cabbage looper) | 
| 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 / Number of copies: 1 / Enantiomer: LEVO | 
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| Source (natural) | Organism:  Homo sapiens (human) | 
| Molecular weight | Theoretical: 51.767242 KDa | 
| Recombinant expression | Organism:   Spodoptera frugiperda (fall armyworm) | 
| Sequence | String: MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGTQQRD EVWVVGMGIV MSLIVLAIVF  GNVLVITAI AKFERLQTVT NYFITSLACA DLVMGLAVVP FGAAHILTKT WTFGNFWCEF WTSIDVLCVT ASIETLCVIA V DRYFAITS  ...String: MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGTQQRD EVWVVGMGIV MSLIVLAIVF  GNVLVITAI AKFERLQTVT NYFITSLACA DLVMGLAVVP FGAAHILTKT WTFGNFWCEF WTSIDVLCVT ASIETLCVIA V DRYFAITS PFKYQSLLTK NKARVIILMV WIVSGLTSFL PIQMHWYRAT HQEAINCYAE ETCCDFFTNQ AYAIASSIVS FY VPLVIMV FVYSRVFQEA KRQLQKIDKS EGRFHVQNLS QVEQDGRTGH GLRRSSKFCL KEHKALKTLG IIMGTFTLCW LPF FIVNIV HVIQDNLIRK EVYILLNWIG YVNSGFNPLI YCRSPDFRIA FQELLCLRRS SLKAYGNGYS SNGNTGEQSG LEVL FQGPY HVEQEKENKL LAEDLPGTED FVGHQGTVPS DNIDSQGRNA STNDSLLETS QVAPA UniProtKB: Beta-2 adrenergic receptor | 
-Macromolecule #5: (5R,6R)-6-(methylamino)-5,6,7,8-tetrahydronaphthalene-1,2,5-triol
| Macromolecule | Name: (5R,6R)-6-(methylamino)-5,6,7,8-tetrahydronaphthalene-1,2,5-triol type: ligand / ID: 5 / Number of copies: 1 / Formula: G1I | 
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| Molecular weight | Theoretical: 209.242 Da | 
| Chemical component information |  ChemComp-G1I:  | 
-Macromolecule #6: water
| Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH | 
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| Molecular weight | Theoretical: 18.015 Da | 
| Chemical component information |  ChemComp-HOH:  | 
-Experimental details
-Structure determination
| Method | cryo EM | 
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|  Processing | single particle reconstruction | 
| Aggregation state | particle | 
- Sample preparation
Sample preparation
| Buffer | pH: 7.5 | 
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| Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY | 
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | 
- Electron microscopy
Electron microscopy
| Microscope | FEI TITAN KRIOS | 
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2 | 
| Electron beam | Acceleration voltage: 300 kV / Electron source:  FIELD EMISSION GUN | 
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm | 
| Sample stage | Cooling holder cryogen: NITROGEN | 
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company | 
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