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- PDB-7dhr: Cryo-EM structure of the full agonist isoprenaline-bound beta2 ad... -

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Basic information

Entry
Database: PDB / ID: 7dhr
TitleCryo-EM structure of the full agonist isoprenaline-bound beta2 adrenergic receptor-Gs protein complex.
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Beta-2 adrenergic receptor
  • Nb35 nanobody
KeywordsSIGNALING PROTEIN / G protein coupled receptor / Isoprenaline / Complex / Cryo-EM
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 / desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / Activation of G protein gated Potassium channels / G-protein activation ...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 / desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / 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 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / positive regulation of cAMP-dependent protein kinase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / norepinephrine binding / Thrombin signalling through proteinase activated receptors (PARs) / Adrenoceptors / heat generation / Ca2+ pathway / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / G alpha (q) signalling events / positive regulation of lipophagy / response to psychosocial stress / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of multicellular organism growth / Vasopressin regulates renal water homeostasis via Aquaporins / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / PKA activation in glucagon signalling / hair follicle placode formation / intracellular transport / adenylate cyclase binding / D1 dopamine receptor binding / smooth muscle contraction / developmental growth / potassium channel regulator activity / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / positive regulation of bone mineralization / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / bone resorption / activation of adenylate cyclase activity / receptor-mediated endocytosis / adenylate cyclase activator activity / response to cold / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / bone development / positive regulation of protein serine/threonine kinase activity / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / platelet aggregation / cognition / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / GPER1 signaling / cellular response to amyloid-beta / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / sensory perception of smell / Cargo recognition for clathrin-mediated endocytosis / retina development in camera-type eye / GTPase binding / Clathrin-mediated endocytosis
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit ...Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ISOPRENALINE / Beta-2 adrenergic receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang, F. / Ling, S.L. / Zhou, Y.X. / Zhang, Y.N. / Lv, P. / Liu, S.L. / Fang, W. / Sun, W.J. / Hu, L.Y.A.
CitationJournal: Natl Sci Rev / Year: 2020
Title: Different Conformational Responses of the beta2-Adrenergic Receptor-Gs Complex upon Binding of the Partial Agonist Salbutamol or the Full Agonist Isoprenaline
Authors: Yang, F. / Ling, S.L. / Zhou, Y.X. / Zhang, Y.N. / Lv, P. / Liu, S.L. / Fang, W. / Sun, W.J. / Hu, L.Y.A. / Zhang, L. / Shi, P. / Tian, C.
History
DepositionNov 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-30682
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nb35 nanobody
R: Beta-2 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,2596
Polymers151,0485
Non-polymers2111
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10810 Å2
ΔGint-79 kcal/mol
Surface area42030 Å2

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#1: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 45725.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63092
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62871
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 8805.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63212

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Antibody / Protein / Non-polymers , 3 types, 3 molecules NR

#4: Antibody Nb35 nanobody


Mass: 17057.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Protein Beta-2 adrenergic receptor / / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 42042.906 Da / Num. of mol.: 1
Mutation: G16R,E27Q,C77V,M96T,M98T,E122W,C125V,N187E,C265A,C285A,C327S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550
#6: Chemical ChemComp-5FW / ISOPRENALINE / Isoprenaline


Mass: 211.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, agonist*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the full agonist isoprenaline-bound beta2 adrenergic receptor-Gs protein complex.
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 151.40 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD
Image recordingElectron dose: 57.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231827 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7BZ2

7bz2

RefinementCross valid method: NONE / Stereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00397204
ELECTRON MICROSCOPYf_angle_d0.82579845
ELECTRON MICROSCOPYf_chiral_restr0.05151180
ELECTRON MICROSCOPYf_plane_restr0.00581240
ELECTRON MICROSCOPYf_dihedral_angle_d4.74954156

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