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

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Basic information

Entry
Database: PDB / ID: 9pln
TitleLocally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905)
ComponentsAlpha-2A adrenergic receptor
KeywordsMEMBRANE PROTEIN / Receptor / Drug / Complex / GPCR / G-protein / scFv16
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: 2.8 Å
AuthorsSrinivasan, K. / Xu, X. / Mailhot, O. / Manglik, A. / Shoichet, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
CitationJournal: To Be Published
Title: Toward a Random Background for Ligand Optimization
Authors: Xu, X. / Mailhot, O. / Correy, G. / Huang, X.P. / Braz, J. / Shi, D. / Srinivasan, K. / Holota, Y. / Kuziv, Y. / Tsoutsouvas, C. / Levinzon, N. / Doruk, Y.U. / Rachman, M. / Diolaiti, M. / ...Authors: Xu, X. / Mailhot, O. / Correy, G. / Huang, X.P. / Braz, J. / Shi, D. / Srinivasan, K. / Holota, Y. / Kuziv, Y. / Tsoutsouvas, C. / Levinzon, N. / Doruk, Y.U. / Rachman, M. / Diolaiti, M. / Stevens, M. / Liu, F. / Hubner, H. / Wang, J. / Wu, Y. / Ashworth, A. / Makriyannis, A. / Zhang, Y. / Moroz, Y. / Gmeiner, P. / Abel, R. / Manglik, A. / Basbaum, A. / Roth, B. / Fraser, J. / Shoichet, B.
History
DepositionJul 15, 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: Additional map / Part number: 1 / Data content type: Additional map / 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: Mask / Part number: 1 / Data content type: Mask / 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)53,8782
Polymers53,6441
Non-polymers2341
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-A1CIU / N-(5-methylnaphthalen-1-yl)pyridin-4-amine


Mass: 234.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2 / 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 4905.
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: CHS was solubilized in LMNG and GDN prior to diluting into buffers.
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMSodium chlorideNaCl1
30.0075 % w/vLauryl Maltose Neopentyl GlycolC47H88O221
40.0025 % w/vGlyco-diosgeninC56H92O251
50.001 % w/vCholesteryl hemisuccinateC31H50O41
60.01 mMN-(5-methylnaphthalen-1-yl)pyridin-4-amineC16H14N21
SpecimenConc.: 2.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA current / Grid 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 magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 0.596 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10305

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9PHENIX1.21.2_5419:model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6609807
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 323827 / Symmetry type: POINT
Atomic model buildingB value: 110.6 / Protocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7EJ8

7ej8


Accession code: 7EJ8 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038833
ELECTRON MICROSCOPYf_angle_d0.55711963
ELECTRON MICROSCOPYf_dihedral_angle_d4.1721195
ELECTRON MICROSCOPYf_chiral_restr0.0391353
ELECTRON MICROSCOPYf_plane_restr0.0031508

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