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- PDB-6kux: Crystal structures of the alpha2A adrenergic receptor in complex ... -

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Basic information

Entry
Database: PDB / ID: 6kux
TitleCrystal structures of the alpha2A adrenergic receptor in complex with an antagonist RSC.
Componentsalpha2A adrenergic receptor
KeywordsSIGNALING PROTEIN / alpha2A adrenergic receptor / antagonist / GPCR
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 / dopaminergic synapse / positive regulation of potassium ion transport / 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 / negative regulation of insulin secretion / female pregnancy / 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 / Cytochrome c/b562 / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) ...Alpha 2A adrenoceptor / Cytochrome c/b562 / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-E3F / CITRATE ANION / OLEIC ACID / DI(HYDROXYETHYL)ETHER / Alpha-2A adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsQu, L. / Zhou, Q.T. / Wu, D. / Zhao, S.W.
CitationJournal: To Be Published
Title: Crystal structures of the alpha2A adrenergic receptor in complex with an antagonist RSC.
Authors: Qu, L. / Zhou, Q.T. / Wu, D. / Zhao, S.W.
History
DepositionSep 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha2A adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8589
Polymers44,4911
Non-polymers1,3678
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-1 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.170, 71.790, 284.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein alpha2A adrenergic receptor


Mass: 44490.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08913*PLUS
#2: Chemical ChemComp-E3F / (8~{a}~{R},12~{a}~{S},13~{a}~{S})-12-ethylsulfonyl-3-methoxy-5,6,8,8~{a},9,10,11,12~{a},13,13~{a}-decahydroisoquinolino[2,1-g][1,6]naphthyridine


Mass: 364.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N2O3S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.0, 290mM Ammonium chloride, 30% PEG400, 7% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→49.7 Å / Num. obs: 18743 / % possible obs: 91.4 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.487 / Num. unique obs: 2155 / CC1/2: 0.46 / % possible all: 73.4
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y02

2y02


Resolution: 2.7→47.385 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.41
RfactorNum. reflection% reflection
Rfree0.2669 867 4.63 %
Rwork0.2511 --
obs0.252 18724 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 79 0 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033043
X-RAY DIFFRACTIONf_angle_d0.5264135
X-RAY DIFFRACTIONf_dihedral_angle_d15.6421802
X-RAY DIFFRACTIONf_chiral_restr0.039487
X-RAY DIFFRACTIONf_plane_restr0.003508
LS refinement shellResolution: 2.7→2.8691 Å
RfactorNum. reflection% reflection
Rfree0.2669 109 -
Rwork0.2511 2332 -
obs--73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.88630.62151.08990.27591.52256.0010.0278-0.96940.10750.18970.55630.0659-1.14641.7109-0.22381.7608-0.18290.18121.4739-0.51170.7221-2.3629-4.9629-33.3038
26.75892.12120.95627.9903-0.10523.92720.02680.0133-0.14150.1850.08380.17860.2116-0.2315-0.13690.3097-0.0049-0.00750.3075-0.01090.7441-11.3049-34.386-70.0184
34.6540.1353.77810.5670.16792.6944-0.1833-0.0066-0.18160.8070.343-0.53681.51692.9610.05281.75870.33650.02471.6924-0.42920.83470.0879-15.3426-35.5685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 227 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1001 through 1106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 443 )

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