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- PDB-9pqd: Locally-refined structure of alpha2a adrenergic receptor in compl... -

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Basic information

Entry
Database: PDB / ID: 9pqd
TitleLocally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound Z7149
ComponentsAlpha-2A adrenergic receptor
KeywordsMEMBRANE PROTEIN / GPCR / Complex / Drug / Small Molecule / Polypharmacology
Function / homology
Function and homology information


negative regulation of uterine smooth muscle contraction / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / alpha-2C adrenergic receptor binding / epinephrine binding / phospholipase C-activating adrenergic receptor signaling pathway / negative regulation of norepinephrine secretion / alpha-1B adrenergic receptor binding / negative regulation of epinephrine secretion ...negative regulation of uterine smooth muscle contraction / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / alpha-2C adrenergic receptor binding / epinephrine binding / phospholipase C-activating adrenergic receptor signaling pathway / negative regulation of norepinephrine secretion / alpha-1B adrenergic receptor binding / negative regulation of epinephrine secretion / heterotrimeric G-protein binding / negative regulation of calcium ion-dependent exocytosis / Surfactant metabolism / positive regulation of potassium ion transport / dopaminergic synapse / thermoception / fear response / thioesterase binding / negative regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of membrane protein ectodomain proteolysis / norepinephrine binding / Adrenoceptors / intestinal absorption / response to alcohol / positive regulation of epidermal growth factor receptor signaling pathway / response to morphine / positive regulation of wound healing / adrenergic receptor signaling pathway / negative regulation of calcium ion transport / regulation of vasoconstriction / negative regulation of lipid catabolic process / Rho protein signal transduction / cellular response to hormone stimulus / adenylate cyclase-activating adrenergic receptor signaling pathway / presynaptic active zone membrane / axon terminus / presynaptic modulation of chemical synaptic transmission / guanyl-nucleotide exchange factor activity / positive regulation of cytokine production / female pregnancy / negative regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / postsynaptic density membrane / GABA-ergic synapse / platelet activation / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / glucose homeostasis / actin cytoskeleton organization / G alpha (i) signalling events / basolateral plasma membrane / Ras protein signal transduction / DNA replication / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / protein heterodimerization activity / neuronal cell body / positive regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Alpha 2A adrenoceptor / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / 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)
Similarity search - Domain/homology
: / Alpha-2A adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSrinivasan, K. / Wu, Y. / Billesboelle, C. / Kim, J.Y. / Manglik, A. / Shoichet, B.K.
Funding support United States, 2items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011-19-2-0020 United States
Department of Health & Human Services (HHS)1AY1AX000035 United States
CitationJournal: To Be Published
Title: Large library docking for polypharmacology
Authors: Wu, Y. / Vigneron, S. / Huang, X. / Braz, J. / Srinivasan, K. / Fink, E. / Xu, X. / Huebner, H. / Billesboelle, C. / Kim, J.Y. / Wang, J. / Pfeiffer, T. / Sakamoto, K. / Radchenko, D. / ...Authors: Wu, Y. / Vigneron, S. / Huang, X. / Braz, J. / Srinivasan, K. / Fink, E. / Xu, X. / Huebner, H. / Billesboelle, C. / Kim, J.Y. / Wang, J. / Pfeiffer, T. / Sakamoto, K. / Radchenko, D. / Moroz, Y. / Irwin, J. / Gmeiner, P. / Roth, B. / Basbaum, A. / Manglik, A. / Wetsel, W. / Shoichet, B.K.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Alpha-2A adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8562
Polymers53,6441
Non-polymers2121
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Alpha-2A adrenergic receptor / Alpha-2 adrenergic receptor subtype C10 / Alpha-2A adrenoreceptor / Alpha-2A adrenoceptor / Alpha-2AAR


Mass: 53643.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRA2A, ADRA2R, ADRAR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08913
#2: Chemical ChemComp-A1CIZ / (6M)-1-methyl-6-(1,2,5,6-tetrahydropyridin-3-yl)-1H-indole


Mass: 212.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound Z7149
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Details: Buffer was supplemented with 0.01 mM compound Z7149
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepesC8H18N2O4S1
2100 mMSodium chlorideNaCl1
30.0075 % w/vLMNGC47H88O221
40.0025 % w/vGDNC56H92O251
50.001 % w/vCHSC31H50O41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 47.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38025 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7EJ8

7ej8


Pdb chain-ID: D / Accession code: 7EJ8 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0042218
ELECTRON MICROSCOPYf_angle_d0.6193020
ELECTRON MICROSCOPYf_dihedral_angle_d10.127300
ELECTRON MICROSCOPYf_chiral_restr0.042353
ELECTRON MICROSCOPYf_plane_restr0.004357

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